PDB-6cb7: CRYSTAL STRUCTURE OF VACCINIA VIRUS A6 N-TERMINUS (SPACE GROUP C2)

ID or keywords:

Entry

Database: PDB / ID: 6cb7

Title

CRYSTAL STRUCTURE OF VACCINIA VIRUS A6 N-TERMINUS (SPACE GROUP C2)

Components

Protein A6

Keywords

VIRAL PROTEIN /

VACCINIA VIRUS / A6 / POXVIRUSES / VIRION CORE PROTEIN / VIRION MORPHOGENESIS

Function / homology

Poxvirus A6 / Poxvirus A6 protein /

virion component / NICKEL (II) ION / Protein A6

Function and homology information

Biological species

Vaccinia virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Han, Y. / Zhang, B. / Deng, J.

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of a lipid-bound viral membrane assembly protein reveals a modality for enclosing the lipid bilayer.
Authors: Pathak, P.K. / Peng, S. / Meng, X. / Han, Y. / Zhang, B. / Zhang, F. / Xiang, Y. / Deng, J.

History

Deposition	Feb 2, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 12, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6cb7.cif.gz	67.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6cb7.ent.gz	49.3 KB	Display	PDB format
PDBx/mmJSON format	6cb7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cb/6cb7 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/6cb7	HTTPS FTP

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Related structure data

Related structure data	6br8C 6br9C 6cb6SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4my6-2 5kza-d 5m6l-d 4h87-3 6tfb-2 4uxm-d 2hwn-1 1d6t-d 4bf8-d 4gj4-4 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

Deposited unit

A: Protein A6

hetero molecules

14.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	42.835, 42.835, 147.950
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-346- HOH
2	1	A-412- HOH
3	1	A-428- HOH
4	1	A-429- HOH

#1: Protein	Protein A6 Mass: 14049.336 Da / Num. of mol.: 1 / Mutation: E47A, K48A, K49A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus (strain Copenhagen) / Strain: Copenhagen / Gene: A6L / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 GOLD / References: UniProt: P20985
#2: Chemical	ChemComp-NI / NICKEL (II) ION / Nickel Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.39 Å³/Da / Density % sol: 48.44 %
Crystal grow	Temperature: 293 K / Method: evaporation / Details: 0.01M NICL2, 0.1M TRIS PH8.5 20% PEG2000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 33647 / % possible obs: 96.3 % / Redundancy: 11.7 % / R_sym value: 0.069 / Net I/σ(I): 34.9
Reflection shell	Resolution: 1.6→1.66 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 6.1 / R_sym value: 0.58 / % possible all: 78.4

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Processing

Software

Name	Version	Classification
PHENIX	1.6_289	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6CB6

6cb6

Resolution: 1.6→30.289 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 0.1 / Phase error: 17.68

	R_factor	Num. reflection	% reflection
R_free	0.1895	3314	10.02 %
R_work	0.1661	-	-
obs	0.1686	33073	94.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / B_sol: 40.732 Å² / k_sol: 0.351 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.6744 Å²	0 Å²	-0 Å²
2-	-	1.6744 Å²	0 Å²
3-	-	-	-3.3487 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→30.289 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	956	0	1	148	1105

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	991
X-RAY DIFFRACTION	f_angle_d	0.904	1346
X-RAY DIFFRACTION	f_dihedral_angle_d	14.352	363
X-RAY DIFFRACTION	f_chiral_restr	0.064	161
X-RAY DIFFRACTION	f_plane_restr	0.005	166

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.5972-1.6542	0.212	249	0.1807	2211	X-RAY DIFFRACTION	71
1.6542-1.7205	0.1946	316	0.1695	2848	X-RAY DIFFRACTION	91
1.7205-1.7988	0.222	322	0.1655	3008	X-RAY DIFFRACTION	96
1.7988-1.8936	0.2141	339	0.1643	3048	X-RAY DIFFRACTION	97
1.8936-2.0122	0.1925	332	0.1584	3070	X-RAY DIFFRACTION	98
2.0122-2.1675	0.1695	353	0.1492	3109	X-RAY DIFFRACTION	99
2.1675-2.3856	0.2001	341	0.1545	3113	X-RAY DIFFRACTION	99
2.3856-2.7306	0.1691	352	0.1645	3101	X-RAY DIFFRACTION	99
2.7306-3.4395	0.2044	346	0.178	3142	X-RAY DIFFRACTION	100
3.4395-30.2944	0.1691	364	0.1562	3109	X-RAY DIFFRACTION	99

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	5.8942	-1.1586	-1.9533	1.4419	-2.9507	9.7638	-0.307	-0.1209	-0.2076	-0.4088	0.1906	0.2064	1.0983	0.027	0.1288	0.1596	0.0033	0.015	0.1012	0.0039	0.1373	3.2865	-27.8708	16.2637
2	0.2675	0.0435	-0.1054	3.3465	-1.6103	1.1576	-0.0071	-0.0303	0.1574	0.1675	-0.0056	0.4682	-0.2075	-0.114	0.0166	0.1508	0.0018	-0.0066	0.1332	-0.0023	0.181	2.081	-20.1952	11.0411
3	3.147	-1.1288	1.7881	0.7763	-0.6621	6.4938	0.0231	0.0127	0.5329	0.0945	-0.2329	0.1538	-0.3164	-0.5065	0.1622	0.1804	0.0404	-0.0133	0.1708	-0.0051	0.1834	0.0806	-13.3805	3.8681
4	3.2328	-1.1648	1.7864	2.1791	-4.3076	8.7128	-0.035	0.2503	0.6715	-0.17	-0.2107	0.2843	-0.7961	-0.39	0.1312	0.293	0.0853	-0.0631	0.2213	0.0405	0.2339	-2.6885	-11.8037	-2.9457
5	0.033	-0.0342	-0.2325	3.7638	-1.1238	3.8908	-0.0278	-0.0418	-0.3647	0.0756	0.0917	0.5038	0.1853	-0.4715	-0.0283	0.141	-0.0158	-0.0129	0.1645	-0.022	0.2099	1.1085	-28.2745	3.5366
6	5.0205	-0.383	-0.0211	0.4317	0.9675	2.5931	-0.2102	-0.1163	-0.313	-0.0343	0.0458	0.2612	0.2562	-0.1262	0.0727	0.1371	0.0075	-0.0288	0.0961	-0.0039	0.1521	13.3639	-28.5467	4.8902
7	0.4982	0.6565	0.6093	2.2873	-0.034	1.1682	0.0535	-0.0687	0.0288	0.0954	0.0455	-0.212	-0.1915	0.2214	-0.0457	0.1365	-0.0133	0.0177	0.1588	-0.0121	0.1444	22.0925	-21.7198	9.2889
8	3.3161	-0.4844	-0.4134	0.9953	-1.8015	4.0298	-0.0288	0.0937	0.5298	0.169	-0.1292	-0.4878	-0.9098	0.5138	0.0548	0.2026	-0.0627	0.0022	0.1133	-0.0019	0.1689	21.3287	-13.4708	13.4024
9	2.1707	0.5024	-0.5445	1.2774	-0.3344	0.4935	0.1347	0.2601	0.0373	-0.1173	-0.0492	-0.0082	-0.0534	0.048	-0.0711	0.1638	-0.0129	0.0231	0.1387	-0.003	0.1451	16.9004	-14.477	5.505
10	1.4222	-0.1119	0.2028	0.102	0.315	1.1292	0.1147	-0.0242	-0.0727	-0.0984	-0.0791	0.0033	-0.2538	-0.0871	-0.0303	0.1705	0.0151	-0.0045	0.1255	-0.0182	0.1233	11.148	-19.5432	-0.9932
11	2.75	-0.5776	1.7288	0.1767	-0.3787	1.9377	0.0381	0.2397	-0.1623	0.024	-0.0959	0.2221	-0.3797	-0.1604	0.0563	0.1627	0.0088	-0.0278	0.1825	-0.0259	0.1958	2.4852	-21.6003	-0.5358
12	1.4417	-0.6113	-1.1589	1.7229	1.4755	1.5906	0.2768	0.5272	-0.091	-0.0281	-0.2031	-0.1643	-0.3721	-0.2809	0.0185	0.2587	0.0304	-0.059	0.2288	-0.0514	0.1147	4.157	-20.2006	-6.6778
13	0.3091	-0.6208	-0.0788	5.6292	3.0827	1.9487	0.1098	0.0512	0.0668	-0.6861	0.0222	-0.2922	-0.6858	-0.0338	-0.1183	0.2401	0.0177	0.0151	0.0718	0.0065	0.1094	8.731	-7.7743	5.4912
14	0.3774	-0.1959	0.0369	1.4967	0.8582	0.6153	0.0753	-0.2176	0.211	0.3266	-0.1135	0.1903	-0.0201	0.1114	-0.0124	0.1547	0.0107	0.0031	0.0787	-0.0186	0.1289	7.9669	-7.723	13.8771
15	1.5476	-0.2196	0.6633	0.7718	-0.8619	2.0765	0.0459	-0.174	0.1403	-0.0431	-0.1609	0.0689	-0.1764	-0.1382	0.0927	0.1481	0.0038	-0.0014	0.0852	0.0047	0.1085	11.1142	-16.6285	13.177
16	0.5252	0.4749	-0.457	0.7386	-1.0036	1.9821	0.0123	0.0301	0.0756	0.1142	0.0742	0.3305	-0.015	-0.233	-0.0637	0.1476	-0.0013	-0.0036	0.0993	-0.0016	0.1159	12.8542	-25.7297	13.5303
17	4.6235	-4.4902	-0.35	8.3743	0.5154	0.9415	0.0638	-0.099	-0.6635	-0.1122	-0.1761	0.2247	0.1648	0.6282	0.0516	0.2527	0.0398	0.0303	0.1693	0.0275	0.1339	17.1679	-33.9668	13.257

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:5)
2	X-RAY DIFFRACTION	2	(chain A and resid 6:13)
3	X-RAY DIFFRACTION	3	(chain A and resid 14:19)
4	X-RAY DIFFRACTION	4	(chain A and resid 20:27)
5	X-RAY DIFFRACTION	5	(chain A and resid 28:36)
6	X-RAY DIFFRACTION	6	(chain A and resid 37:44)
7	X-RAY DIFFRACTION	7	(chain A and resid 45:55)
8	X-RAY DIFFRACTION	8	(chain A and resid 56:61)
9	X-RAY DIFFRACTION	9	(chain A and resid 62:67)
10	X-RAY DIFFRACTION	10	(chain A and resid 68:73)
11	X-RAY DIFFRACTION	11	(chain A and resid 74:77)
12	X-RAY DIFFRACTION	12	(chain A and resid 78:83)
13	X-RAY DIFFRACTION	13	(chain A and resid 84:94)
14	X-RAY DIFFRACTION	14	(chain A and resid 95:99)
15	X-RAY DIFFRACTION	15	(chain A and resid 100:106)
16	X-RAY DIFFRACTION	16	(chain A and resid 107:112)
17	X-RAY DIFFRACTION	17	(chain A and resid 113:117)

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