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- PDB-6a7s: Ca2+-independent C-type lectin SPL-2 from Saxidomus purpuratus -

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Basic information

Entry
Database: PDB / ID: 6a7s
TitleCa2+-independent C-type lectin SPL-2 from Saxidomus purpuratus
ComponentsN-acetylglucosamine-specific lectin
KeywordsSUGAR BINDING PROTEIN / SPL-2 / lectin / bivalve / Saxidomus purpuratus / C-type
Function / homologyLectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / carbohydrate binding / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetylglucosamine-specific lectin
Function and homology information
Biological speciesSaxidomus purpuratus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsUnno, H. / Hatakeyama, T.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25450133 Japan
Japan Society for the Promotion of Science17K07760 Japan
Japan Society for the Promotion of Science26450128 Japan
Japan Society for the Promotion of Science15K06977 Japan
CitationJournal: Protein Sci. / Year: 2019
Title: Novel Ca2+-independent carbohydrate recognition of the C-type lectins, SPL-1 and SPL-2, from the bivalve Saxidomus purpuratus.
Authors: Unno, H. / Itakura, S. / Higuchi, S. / Goda, S. / Yamaguchi, K. / Hatakeyama, T.
History
DepositionJul 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity_name_com / struct
Item: _struct.pdbx_descriptor
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: N-acetylglucosamine-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3785
Polymers17,8991
Non-polymers4794
Water1,56787
1
B: N-acetylglucosamine-specific lectin
hetero molecules

B: N-acetylglucosamine-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,75710
Polymers35,7982
Non-polymers9598
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2900 Å2
ΔGint-34 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.235, 91.235, 48.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-361-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules B

#1: Protein N-acetylglucosamine-specific lectin


Mass: 17898.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saxidomus purpuratus (invertebrata) / References: UniProt: A0A2Z6G7U3
#2: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 90 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl (pH8.5), 30% PEG4000, 100 mM GalNAc, 10 mM CaCl2

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16065 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 39.6
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.462

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.72 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.46 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20745 765 4.8 %RANDOM
Rwork0.17943 ---
obs0.18079 15278 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.559 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→30.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 29 87 1222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0141172
X-RAY DIFFRACTIONr_bond_other_d0.0010.018928
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.6721592
X-RAY DIFFRACTIONr_angle_other_deg1.1751.6922187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.285137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18824.0367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32215171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.149154
X-RAY DIFFRACTIONr_chiral_restr0.1280.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021330
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02251
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6873.855552
X-RAY DIFFRACTIONr_mcbond_other3.673.846550
X-RAY DIFFRACTIONr_mcangle_it4.6965.759687
X-RAY DIFFRACTIONr_mcangle_other4.6935.769688
X-RAY DIFFRACTIONr_scbond_it4.3484.233620
X-RAY DIFFRACTIONr_scbond_other4.2084.201616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8866.15900
X-RAY DIFFRACTIONr_long_range_B_refined7.3944.6941401
X-RAY DIFFRACTIONr_long_range_B_other7.38344.6021394
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 50 -
Rwork0.26 1087 -
obs--98.1 %

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