PDB-4por: Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'...

ID or keywords:

Entry

Database: PDB / ID: 4por

Title

Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactose

Components

VP1

Keywords

VIRAL PROTEIN /

jelly roll fold / capsid formation / receptor interaction /

carbohydrate / sialyloligosaccharide /

viral coat protein

Function / homology

Function and homology information

T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity /

metal ion binding
Similarity search - Function

Biological species

Human polyomavirus 9

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.09 Å

Authors

Khan, Z.M. / Stehle, T.

Citation

Journal: J.Virol. / Year: 2014
Title: Crystallographic and glycan microarray analysis of human polyomavirus 9 VP1 identifies N-glycolyl neuraminic acid as a receptor candidate.
Authors: Khan, Z.M. / Liu, Y. / Neu, U. / Gilbert, M. / Ehlers, B. / Feizi, T. / Stehle, T.

History

Deposition	Feb 26, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 9, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 26, 2014	Group: Database references
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/po/4por ftp://data.pdbj.org/pub/pdb/validation_reports/po/4por	HTTPS FTP

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Related structure data

Related structure data	4poqSC 4posC 4potC 4fmi 4mby S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4pos-1 4pot-2 3bwq-d 6y66-1 6y65-1 4pos-2 6hku-1 4poq-2 4poq-1 1cn3-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#47 - Nov 2003 Simian Virus 40 similarity (4) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (5) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

F: VP1

G: VP1

H: VP1

I: VP1

J: VP1

hetero molecules

310 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: VP1

B: VP1

C: VP1

D: VP1

E: VP1

hetero molecules

defined by author&software
155 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: VP1

G: VP1

H: VP1

I: VP1

J: VP1

hetero molecules

defined by author&software
155 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	97.010, 180.400, 199.660
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	ALA	ALA	A	A	46 - 50	20 - 24
2	1	THR	THR	ALA	ALA	B	B	46 - 50	20 - 24
3	1	THR	THR	ALA	ALA	C	C	46 - 50	20 - 24
4	1	THR	THR	ALA	ALA	D	D	46 - 50	20 - 24
5	1	THR	THR	ALA	ALA	E	E	46 - 50	20 - 24
6	1	THR	THR	ALA	ALA	F	F	46 - 50	20 - 24
7	1	THR	THR	ALA	ALA	G	G	46 - 50	20 - 24
8	1	THR	THR	ALA	ALA	H	H	46 - 50	20 - 24
9	1	THR	THR	ALA	ALA	I	I	46 - 50	20 - 24
10	1	THR	THR	ALA	ALA	J	J	46 - 50	20 - 24
1	2	GLY	GLY	GLY	GLY	A	A	140 - 160	114 - 134
2	2	GLY	GLY	GLY	GLY	B	B	140 - 160	114 - 134
3	2	GLY	GLY	GLY	GLY	C	C	140 - 160	114 - 134
4	2	GLY	GLY	GLY	GLY	D	D	140 - 160	114 - 134
5	2	GLY	GLY	GLY	GLY	E	E	140 - 160	114 - 134
6	2	GLY	GLY	GLY	GLY	F	F	140 - 160	114 - 134
7	2	GLY	GLY	GLY	GLY	G	G	140 - 160	114 - 134
8	2	GLY	GLY	GLY	GLY	H	H	140 - 160	114 - 134
9	2	GLY	GLY	GLY	GLY	I	I	140 - 160	114 - 134
10	2	GLY	GLY	GLY	GLY	J	J	140 - 160	114 - 134
1	3	ASP	ASP	VAL	VAL	A	A	250 - 268	224 - 242
2	3	ASP	ASP	VAL	VAL	B	B	250 - 268	224 - 242
3	3	ASP	ASP	VAL	VAL	C	C	250 - 268	224 - 242
4	3	ASP	ASP	VAL	VAL	D	D	250 - 268	224 - 242
5	3	ASP	ASP	VAL	VAL	E	E	250 - 268	224 - 242
6	3	ASP	ASP	VAL	VAL	F	F	250 - 268	224 - 242
7	3	ASP	ASP	VAL	VAL	G	G	250 - 268	224 - 242
8	3	ASP	ASP	VAL	VAL	H	H	250 - 268	224 - 242
9	3	ASP	ASP	VAL	VAL	I	I	250 - 268	224 - 242
10	3	ASP	ASP	VAL	VAL	J	J	250 - 268	224 - 242
1	4	SER	SER	PRO	PRO	A	A	280 - 287	254 - 261
2	4	SER	SER	PRO	PRO	B	B	280 - 287	254 - 261
3	4	SER	SER	PRO	PRO	C	C	280 - 287	254 - 261
4	4	SER	SER	PRO	PRO	D	D	280 - 287	254 - 261
5	4	SER	SER	PRO	PRO	E	E	280 - 287	254 - 261
6	4	SER	SER	PRO	PRO	F	F	280 - 287	254 - 261
7	4	SER	SER	PRO	PRO	G	G	280 - 287	254 - 261
8	4	SER	SER	PRO	PRO	H	H	280 - 287	254 - 261
9	4	SER	SER	PRO	PRO	I	I	280 - 287	254 - 261
10	4	SER	SER	PRO	PRO	J	J	280 - 287	254 - 261

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(0.314253, 0.743457, -0.590353), (-0.684447, 0.608357, 0.401789), (0.657858, 0.277802, 0.700035)	18.27967, 19.38157, -18.26652
3	given	(-0.802839, 0.512699, -0.304285), (-0.366538, -0.021927, 0.930145), (0.470212, 0.858288, 0.205527)	48.60281, 11.54144, -13.9016
4	given	(-0.801043, -0.368179, 0.47199), (0.511311, -0.010833, 0.859328), (-0.311273, 0.929692, 0.196931)	49.71659, -11.83449, 6.67895
5	given	(0.316074, -0.677636, 0.664008), (0.736562, 0.616399, 0.27844), (-0.597975, 0.401075, 0.693948)	20.30151, -19.39735, 15.65091
6	given	(-0.85658, -0.399039, 0.327168), (-0.386172, 0.075185, -0.919358), (0.342261, -0.913846, -0.218499)	45.70204, -43.64127, -70.69236
7	given	(-0.7633, 0.468768, -0.444557), (0.479834, -0.049406, -0.875967), (-0.432589, -0.881939, -0.187219)	42.01988, -66.78728, -49.92224
8	given	(0.366769, 0.639782, -0.675396), (0.644991, -0.698051, -0.310984), (-0.670423, -0.321565, -0.668677)	11.47617, -70.40061, -44.33149
9	given	(0.990411, -0.133073, -0.03713), (-0.133001, -0.991106, 0.004427), (-0.037389, 0.000554, -0.999301)	-4.21849, -48.99893, -61.88963
10	given	(0.234038, -0.775701, 0.586101), (-0.773104, -0.514027, -0.3716), (0.589522, -0.366149, -0.719999)	17.13765, -32.5425, -78.11585

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Protein / Sugars , 2 types, 19 molecules ABCDEFGHIJ

#1: Protein

VP1 / Major Capsid Protein

Mass: 30157.977 Da / Num. of mol.: 10 / Fragment: UNP residues 32-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human polyomavirus 9 / Gene: gp3, vp1 / Plasmid: pET28a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E9NQ90

#2: Polysaccharide

N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide

/ Mass: 633.552 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DNeup5Aca2-3DGalpb1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2	WURCS	PDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}	LINUCS	PDB-CARE

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Non-polymers , 4 types, 2417 molecules

#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol Mass: 60.095 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2364 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.9 Å³/Da / Density % sol: 57.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.15 Details: 20% v/v isopropanol, 0.2 M calcium chloride, 0.1 M sodium acetate, pH 5.15, soaked in 40 mM 3'-sialyllactose for 25 minutes, cryoprotectant: 25% v/v ethylene glycol, VAPOR DIFFUSION, HANGING ...Details: 20% v/v isopropanol, 0.2 M calcium chloride, 0.1 M sodium acetate, pH 5.15, soaked in 40 mM 3'-sialyllactose for 25 minutes, cryoprotectant: 25% v/v ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal

Density Matthews: 2.9 Å³/Da / Density % sol: 57.54 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.15
Details: 20% v/v isopropanol, 0.2 M calcium chloride, 0.1 M sodium acetate, pH 5.15, soaked in 40 mM 3'-sialyllactose for 25 minutes, cryoprotectant: 25% v/v ethylene glycol, VAPOR DIFFUSION, HANGING ...

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Data collection

Diffraction	Mean temperature: 93 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 1, 2013 / Details: mirrors
Radiation	Monochromator: Bartels Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.09→133.855 Å / Num. all: 204785 / Num. obs: 206909 / % possible obs: 98.97 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.15 % / B_iso Wilson estimate: 29.35 Å² / R_merge(I) obs: 0.15 / Net I/σ(I): 8.36
Reflection shell	Resolution: 2.09→2.14 Å / Redundancy: 2.94 % / R_merge(I) obs: 0.78 / Mean I/σ(I) obs: 1.92 / Num. unique all: 14851 / % possible all: 97.88

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Processing

Software

Name	Version	Classification
RemDAq		data collection
MOLREP		phasing
REFMAC	5.8.0025	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4POQ

4poq

Resolution: 2.09→133.855 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.932 / SU B: 9.728 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2157	10219	5 %	RANDOM
R_work	0.17751	-	-	-
all	0.17944	204785	-	-
obs	0.17944	194566	98.89 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 27.79 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.56 Å²	0 Å²	-0 Å²
2-	-	-0.37 Å²	0 Å²
3-	-	-	-0.19 Å²

Refinement step

Cycle: LAST / Resolution: 2.09→133.855 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20577	0	569	2364	23510

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.02	21630
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.234	1.998	29501
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.316	5	2700
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.774	25.587	843
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.014	15	3451
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.253	15	70
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	3500
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	15969
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.692	1.43	10812
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.229	2.404	13502
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.136	1.67	10818
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	6.135	6.349	35541
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	212	MEDIUM POSITIONAL	0.09	0.5
2	B	212	MEDIUM POSITIONAL	0.08	0.5
3	C	212	MEDIUM POSITIONAL	0.09	0.5
4	D	212	MEDIUM POSITIONAL	0.09	0.5
5	E	212	MEDIUM POSITIONAL	0.09	0.5
6	F	212	MEDIUM POSITIONAL	0.11	0.5
7	G	212	MEDIUM POSITIONAL	0.11	0.5
8	H	212	MEDIUM POSITIONAL	0.11	0.5
9	I	212	MEDIUM POSITIONAL	0.07	0.5
10	J	212	MEDIUM POSITIONAL	0.11	0.5
1	A	169	LOOSE POSITIONAL	0.25	5
2	B	169	LOOSE POSITIONAL	0.2	5
3	C	169	LOOSE POSITIONAL	0.21	5
4	D	169	LOOSE POSITIONAL	0.19	5
5	E	169	LOOSE POSITIONAL	0.18	5
6	F	169	LOOSE POSITIONAL	0.58	5
7	G	169	LOOSE POSITIONAL	0.21	5
8	H	169	LOOSE POSITIONAL	0.24	5
9	I	169	LOOSE POSITIONAL	0.2	5
10	J	169	LOOSE POSITIONAL	0.26	5
1	A	212	MEDIUM THERMAL	1.3	2
2	B	212	MEDIUM THERMAL	0.86	2
3	C	212	MEDIUM THERMAL	1	2
4	D	212	MEDIUM THERMAL	0.93	2
5	E	212	MEDIUM THERMAL	0.94	2
6	F	212	MEDIUM THERMAL	1.54	2
7	G	212	MEDIUM THERMAL	0.99	2
8	H	212	MEDIUM THERMAL	1.03	2
9	I	212	MEDIUM THERMAL	0.73	2
10	J	212	MEDIUM THERMAL	0.7	2
1	A	169	LOOSE THERMAL	2.84	10
2	B	169	LOOSE THERMAL	1.09	10
3	C	169	LOOSE THERMAL	1.58	10
4	D	169	LOOSE THERMAL	0.97	10
5	E	169	LOOSE THERMAL	1.18	10
6	F	169	LOOSE THERMAL	3.86	10
7	G	169	LOOSE THERMAL	1.56	10
8	H	169	LOOSE THERMAL	1.33	10
9	I	169	LOOSE THERMAL	1.17	10
10	J	169	LOOSE THERMAL	1.01	10

LS refinement shell

Resolution: 2.09→2.144 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.305	765	-
R_work	0.28	14051	-
obs	-	14051	97.65 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.5757	0.1906	0.4015	3.3485	4.5078	9.0435	-0.0273	-0.0294	0.1617	-0.3353	0.1026	-0.1324	-0.5838	0.3961	-0.0752	0.1962	-0.0059	-0.0001	0.0764	0.013	0.0755	52.1371	-40.3269	-57.9321
2	0.3581	-0.3384	-0.2639	3.1911	1.2493	1.9654	-0.0183	-0.0483	0.0593	0.0525	0.1961	-0.3724	-0.0821	0.3797	-0.1778	0.1949	0.0404	0.0104	0.1011	-0.0214	0.0476	53.2245	-47.9892	-54.9618
3	0.2308	0.1618	0.0861	0.826	0.1675	0.7544	-0.0009	0.0018	0.0116	0.002	0.0016	-0.0842	0.0312	0.0704	-0.0007	0.2313	0.0354	0.0084	0.0385	-0.0015	0.0134	43.8498	-55.2984	-59.8951
4	1.1799	0.6469	1.0675	2.0998	2.0743	3.3364	0.0026	-0.0495	-0.0072	0.0377	0.097	-0.1531	-0.0285	0.1428	-0.0996	0.2187	0.0267	0.0082	0.0208	-0.006	0.0147	47.3506	-44.5557	-55.0756
5	2.553	3.4102	4.2688	6.3357	7.5749	10.5279	-0.1575	-0.2676	0.331	-0.3733	-0.341	0.4843	-0.7043	-0.4767	0.4985	0.3716	0.0326	-0.0027	0.0928	0.0126	0.081	27.5142	-13.6434	-60.6124
6	0.9868	-0.4267	-0.224	1.2529	0.6388	1.8898	-0.0198	0.0344	0.0836	-0.235	0.0395	-0.1442	-0.3232	0.1785	-0.0197	0.3558	-0.004	-0.0059	0.0675	0.0242	0.0343	31.137	-29.3811	-80.4096
7	0.3774	-0.0239	0.0878	0.5246	0.1435	0.6012	0.0258	0.0258	0.0388	-0.1244	-0.0267	0.002	-0.0741	0.0209	0.0009	0.3031	0.0232	-0.0021	0.0269	0.0099	0.0073	31.4049	-35.7783	-72.7701
8	0.5104	0.5414	0.3104	3.9858	2.5478	2.6792	0.0213	-0.0275	0.0438	-0.1381	0.0269	-0.0769	-0.1441	0.1264	-0.0482	0.2529	0.0218	-0.0094	0.0286	0.0002	0.0128	28.7944	-27.4829	-68.7336
9	2.0586	2.7183	0.8561	11.2621	6.4283	4.2898	0.0077	-0.2646	0.3309	0.5502	-0.327	0.7874	0.2188	-0.3068	0.3194	0.2799	0.0936	-0.027	0.2121	0.0014	0.1724	-2.3864	-24.9048	-48.5067
10	1.1657	0.1309	-0.3969	0.4145	0.1651	2.0595	-0.0204	-0.0336	0.0997	-0.1992	-0.1259	0.2934	-0.2316	-0.3113	0.1464	0.3323	0.0408	-0.1248	0.1593	-0.0572	0.2288	-3.1966	-37.5249	-70.8861
11	0.3952	-0.0002	-0.1435	0.536	0.0224	0.5041	0.0235	0.0056	0.0124	-0.0495	-0.0475	0.1275	-0.0434	-0.1303	0.0241	0.2752	0.0133	-0.0421	0.0851	-0.0043	0.0399	6.1129	-39.0582	-68.0195
12	0.7023	-0.4023	-0.1937	4.026	2.5648	3.0158	0.0358	-0.0005	0.0724	-0.1047	-0.083	0.0488	-0.184	-0.1262	0.0472	0.2049	0.0131	-0.0356	0.0827	0.0133	0.0509	2.0899	-34.7882	-60.5867
13	0.9905	-2.648	-2.2645	11.899	7.2163	5.5986	-0.0878	-0.2157	-0.0137	0.9729	0.1399	0.1299	0.4396	0.2695	-0.0521	0.3363	-0.0937	0.0541	0.2647	0.032	0.1552	3.9067	-50.156	-26.5792
14	0.9637	-0.2051	0.3548	1.8824	0.9865	1.1989	0.0007	-0.0371	-0.1085	0.2298	-0.07	0.3167	0.2382	-0.1996	0.0693	0.3038	-0.0949	0.0403	0.1189	0.0058	0.1545	-1.9448	-66.0712	-47.3057
15	0.4277	-0.2208	-0.0398	0.647	0.1359	0.6671	-0.0098	-0.0319	-0.0532	0.0606	-0.0106	0.1648	0.0554	-0.1633	0.0204	0.2643	-0.0495	0.0157	0.0988	-0.0056	0.0859	3.1018	-58.018	-50.36
16	0.8273	-0.5781	-0.7537	2.5219	2.4714	3.3584	0.0347	-0.056	-0.0022	-0.0351	-0.1177	0.18	-0.0882	-0.2181	0.083	0.2428	-0.0354	0.002	0.0727	0.0315	0.0595	4.3864	-56.0973	-41.4137
17	0.7796	-2.0432	-2.8673	6.567	6.5283	11.6085	0.1237	-0.1988	0.1604	-0.0471	0.3962	-0.5671	-0.5139	0.7383	-0.5199	0.3298	0.0065	-0.032	0.204	-0.001	0.061	37.8225	-54.6288	-25.1289
18	0.9097	0.2288	-0.0934	2.6577	1.4211	1.7037	0.0086	-0.1868	-0.0547	0.3611	0.0147	-0.0059	0.3801	0.0726	-0.0233	0.2931	0.0279	-0.0071	0.071	0.0345	0.024	33.3546	-70.2528	-38.8324
19	0.7275	0.0889	-0.1851	0.4488	-0.1628	0.5272	0.0211	-0.0717	-0.0637	0.0861	-0.018	0.0757	0.1496	-0.0516	-0.0031	0.305	-0.0067	0.0025	0.0368	0.0067	0.0247	26.2371	-67.5334	-46.0607
20	0.5444	0.0604	0.0743	2.4039	2.5057	4.1311	0.0019	-0.0793	-0.0084	0.1973	-0.0555	0.0571	0.1649	-0.0612	0.0536	0.2433	0.0075	-0.0032	0.0254	0.0096	0.0097	32.9042	-63.5155	-38.8602
21	2.5675	-3.625	0.2472	12.0402	6.8004	8.9781	0.3086	0.3496	-0.0579	-1.1423	-0.4654	0.5228	-0.3147	-0.3958	0.1568	0.3447	-0.1401	0.0209	0.2149	0.012	0.2269	-1.408	-29.5402	-17.2781
22	1.1672	-0.097	0.4067	0.8789	0.1197	0.8209	-0.0127	-0.1493	-0.0041	0.1672	0.006	0.2101	0.0362	-0.2712	0.0067	0.3905	-0.0057	0.1192	0.1272	-0.0252	0.1131	1.2095	-6.0257	11.2105
23	0.833	2.1885	-0.7144	26.996	3.938	2.2174	-0.1016	0.132	0.1323	-0.5855	0.006	1.1358	-0.0019	-0.2666	0.0957	0.3177	-0.033	0.0279	0.3037	0.0344	0.2824	-10.4137	-36.7948	-11.0344
24	0.3958	0.2645	0.2537	0.5211	0.1898	0.5891	0.0252	-0.0544	-0.0324	0.1528	-0.0481	0.1324	0.0935	-0.1102	0.0228	0.3407	-0.0016	0.0926	0.102	-0.0111	0.0777	7.3884	-12.7258	3.3761
25	2.7811	3.008	2.1164	8.8959	5.4461	5.1319	-0.1851	0.3716	-0.1206	-0.6795	0.3379	-0.1086	-0.2133	0.2751	-0.1528	0.3112	0.0584	-0.04	0.1653	0.0222	0.0947	6.9455	-0.9303	-36.5602
26	1.0076	-0.0739	-0.1515	1.3077	0.29	1.3938	-0.0127	0.061	0.0668	-0.059	-0.0674	0.2501	-0.1834	-0.247	0.0801	0.295	0.0811	0.0115	0.0981	-0.0194	0.1105	4.5246	16.5595	-13.9354
27	0.3613	0.2053	-0.0119	0.5659	0.2162	0.6911	-0.0228	0.0115	0.0218	0.0365	-0.017	0.157	-0.075	-0.1776	0.0398	0.2627	0.0475	0.0265	0.0714	-0.0155	0.0823	8.4714	7.741	-11.7353
28	0.885	0.8003	0.9643	2.7324	2.3992	3.4445	0.056	-0.0203	-0.0377	0.0042	-0.1322	0.1655	-0.0051	-0.325	0.0762	0.2235	0.0371	0.0315	0.0493	-0.0014	0.0561	8.6855	6.9595	-20.4404
29	3.112	3.4027	5.186	6.1969	6.8665	10.3868	0.1503	0.4016	-0.2902	-0.0323	0.4187	-0.4893	0.3015	0.7196	-0.569	0.295	-0.0304	0.0514	0.161	-0.018	0.0596	40.5996	0.4245	-38.5243
30	1.1576	0.1357	0.4675	1.7572	0.8714	0.9807	-0.0437	0.2178	0.0996	-0.2518	0.159	-0.0814	-0.3076	0.2079	-0.1154	0.3107	-0.044	0.0319	0.0636	-0.0015	0.0494	39.0598	16.4633	-25.188
31	0.6894	-0.1404	0.2572	0.492	-0.1176	0.9612	-0.0236	0.0345	0.0549	0.0147	-0.0007	0.0456	-0.1439	0.0039	0.0242	0.2672	0.0043	0.0132	0.0024	0.003	0.0135	32.1652	14.2092	-16.912
32	0.6513	0.3639	0.5923	2.2279	2.4478	4.8192	-0.042	0.0524	-0.0205	-0.061	0.0288	0.0396	-0.0624	-0.0347	0.0132	0.1894	-0.0062	0.0194	0.0075	-0.001	0.0041	37.8411	9.5365	-24.3858
33	0.7867	0.2633	0.0499	1.9128	2.553	5.8412	-0.036	0.0476	-0.1855	0.3412	0.065	-0.0687	0.5326	0.3375	-0.029	0.2995	0.0783	-0.0332	0.0701	-0.0002	0.0857	54.5011	-15.7186	-5.7269
34	0.3517	0.2792	0.5892	4.0002	1.6606	2.3317	0.034	0.0294	-0.0361	-0.0851	0.3078	-0.6012	0.0919	0.4561	-0.3418	0.2286	-0.0193	-0.0115	0.1808	-0.0415	0.1275	58.5711	-4.8236	-7.1578
35	0.1427	-0.1375	0.0464	0.7186	0.2902	0.8056	-0.0197	-0.0072	-0.0154	0.0851	0.0377	-0.1157	0.0216	0.0855	-0.018	0.2686	0.0073	-0.0233	0.064	-0.0091	0.0394	48.491	-2.0037	-4.8047
36	0.7596	-0.3886	-0.564	2.4175	2.2403	3.4838	0.0329	0.0732	-0.0189	0.0136	0.0653	-0.1572	0.0007	0.0614	-0.0982	0.2392	0.0206	-0.0301	0.0324	-0	0.023	50.239	-11.2505	-8.8091
37	0.9585	-1.2292	-1.6074	5.1943	6.1602	9.2782	-0.0971	-0.0006	-0.1515	0.301	-0.2533	0.3477	0.4802	-0.4033	0.3504	0.4684	-0.0205	0.0308	0.0614	0.0249	0.0602	26.6154	-31.7852	7.8049
38	1.1673	0.2981	0.3095	1.208	0.6068	1.8944	-0.0191	0.0047	-0.1971	0.3542	0.1476	-0.1641	0.4003	0.1056	-0.1285	0.45	0.0382	-0.0018	0.107	0.018	0.0637	35.5987	-25.6822	14.9485
39	0.2918	0.0944	-0.0359	0.5965	0.0948	0.3909	0.003	-0.0544	-0.0561	0.2194	-0.0091	0.0009	0.1119	0.0146	0.0061	0.4042	0.0158	0.0105	0.0587	0.0059	0.012	33.8255	-17.9457	9.4556
40	0.3223	-0.2719	-0.1931	3.871	2.5524	2.5493	-0.002	0.0124	-0.0222	0.1256	0.0678	-0.0964	0.1529	0.1171	-0.0658	0.3536	0.0177	0.0198	0.0629	0.0133	0.0117	30.7788	-26.9426	5.6006

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	34 - 68
2	X-RAY DIFFRACTION	2	A	69 - 122
3	X-RAY DIFFRACTION	3	A	123 - 245
4	X-RAY DIFFRACTION	4	A	246 - 302
5	X-RAY DIFFRACTION	5	B	34 - 53
6	X-RAY DIFFRACTION	6	B	54 - 108
7	X-RAY DIFFRACTION	7	B	109 - 246
8	X-RAY DIFFRACTION	8	B	247 - 302
9	X-RAY DIFFRACTION	9	C	34 - 53
10	X-RAY DIFFRACTION	10	C	54 - 109
11	X-RAY DIFFRACTION	11	C	110 - 247
12	X-RAY DIFFRACTION	12	C	248 - 302
13	X-RAY DIFFRACTION	13	D	34 - 53
14	X-RAY DIFFRACTION	14	D	54 - 106
15	X-RAY DIFFRACTION	15	D	107 - 245
16	X-RAY DIFFRACTION	16	D	246 - 302
17	X-RAY DIFFRACTION	17	E	34 - 53
18	X-RAY DIFFRACTION	18	E	54 - 122
19	X-RAY DIFFRACTION	19	E	123 - 251
20	X-RAY DIFFRACTION	20	E	252 - 302
21	X-RAY DIFFRACTION	21	F	34 - 48
22	X-RAY DIFFRACTION	22	F	49 - 98
23	X-RAY DIFFRACTION	23	F	99 - 109
24	X-RAY DIFFRACTION	24	F	110 - 304
25	X-RAY DIFFRACTION	25	G	34 - 52
26	X-RAY DIFFRACTION	26	G	53 - 109
27	X-RAY DIFFRACTION	27	G	110 - 250
28	X-RAY DIFFRACTION	28	G	251 - 302
29	X-RAY DIFFRACTION	29	H	33 - 53
30	X-RAY DIFFRACTION	30	H	54 - 120
31	X-RAY DIFFRACTION	31	H	121 - 251
32	X-RAY DIFFRACTION	32	H	252 - 302
33	X-RAY DIFFRACTION	33	I	34 - 69
34	X-RAY DIFFRACTION	34	I	70 - 110
35	X-RAY DIFFRACTION	35	I	111 - 245
36	X-RAY DIFFRACTION	36	I	246 - 302
37	X-RAY DIFFRACTION	37	J	33 - 66
38	X-RAY DIFFRACTION	38	J	67 - 108
39	X-RAY DIFFRACTION	39	J	109 - 247
40	X-RAY DIFFRACTION	40	J	248 - 304

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