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- PDB-8wcj: Crystal structure of GB3 penta mutation L5V/K10H/T16S/K19E/Y33I -

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Basic information

Entry
Database: PDB / ID: 8wcj
TitleCrystal structure of GB3 penta mutation L5V/K10H/T16S/K19E/Y33I
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / Immunoglobulin G binding protein G / PROTEIN BINDING
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsQin, M.M. / Chen, X.X. / Zhang, X.Y. / Song, X.F. / Yao, L.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201011 China
CitationJournal: Anal.Chem. / Year: 2024
Title: Protein Allostery Study in Cells Using NMR Spectroscopy.
Authors: Chen, X. / Zhang, X. / Qin, M. / Chen, J. / Wang, M. / Liu, Z. / An, L. / Song, X. / Yao, L.
History
DepositionSep 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,1461
Polymers6,1461
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.130, 70.130, 53.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-178-

HOH

21A-185-

HOH

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Components

#1: Antibody Immunoglobulin G-binding protein G


Mass: 6145.680 Da / Num. of mol.: 1 / Mutation: L446V, K451H, T457S, K460E, Y474I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / References: UniProt: P19909
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 60% v/v Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 10131 / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.022 / Rrim(I) all: 0.075 / Χ2: 1.022 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.55-1.589.90.2594900.970.9920.0880.2741.041100
1.58-1.6110.70.2534970.9820.9950.0820.2661.155100
1.61-1.6411.50.2445030.9780.9950.0760.2551.237100
1.64-1.6712.50.2374970.9860.9960.0710.2471.211100
1.67-1.7112.30.2064960.9860.9960.0620.2161.307100
1.71-1.7512.10.24820.9850.9960.0610.2091.224100
1.75-1.7912.70.1765030.9910.9980.0520.1831.197100
1.79-1.8412.30.1615050.9870.9970.0490.1691.262100
1.84-1.89120.1464930.9910.9980.0440.1531.213100
1.89-1.9512.20.1285070.9940.9980.0390.1341.185100
1.95-2.0212.30.1225030.9960.9990.0370.1271.176100
2.02-2.1120.1144930.990.9970.0350.121.166100
2.1-2.212.50.1034970.9950.9990.0310.1071.054100
2.2-2.3212.10.0985070.990.9980.030.1030.988100
2.32-2.4612.30.0935190.9950.9990.0280.0970.927100
2.46-2.6512.20.0895030.9960.9990.0260.0930.86199.8
2.65-2.9212.80.0755120.9970.9990.0210.0780.75100
2.92-3.34120.0655250.99810.0190.0670.628100
3.34-4.21120.0555250.9980.9990.0170.0580.517100
4.21-5010.90.0485740.9970.9990.0160.0510.44399.7

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→27.06 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 922 10 %
Rwork0.205 --
obs0.2078 9218 92.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→27.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms428 0 0 85 513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01447
X-RAY DIFFRACTIONf_angle_d1.006609
X-RAY DIFFRACTIONf_dihedral_angle_d4.96860
X-RAY DIFFRACTIONf_chiral_restr0.06171
X-RAY DIFFRACTIONf_plane_restr0.00680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.630.2984910.2442813X-RAY DIFFRACTION64
1.63-1.730.25481150.24081045X-RAY DIFFRACTION83
1.73-1.870.27581360.23051222X-RAY DIFFRACTION97
1.87-2.050.24671420.19671278X-RAY DIFFRACTION100
2.05-2.350.25621430.20271280X-RAY DIFFRACTION100
2.35-2.960.25481440.20491300X-RAY DIFFRACTION100
2.96-27.060.18741510.19441358X-RAY DIFFRACTION99

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