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- PDB-7da8: X-ray structure of a GB1:T2Q/D46K mutant -

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Basic information

Entry
Database: PDB / ID: 7da8
TitleX-ray structure of a GB1:T2Q/D46K mutant
ComponentsImmunoglobulin G-binding protein G
KeywordsPROTEIN BINDING / GB1 / T2Q mutant / D46K mutant / X-ray crystal structure / PLANT PROTEIN
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsManjula, R. / Ramaswamy, S. / Gosavi, S.
CitationJournal: To Be Published
Title: X-ray structure of a GB1:T2Q/D46K mutant
Authors: Manjula, R. / Ramaswamy, S. / Gosavi, S.
History
DepositionOct 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)7,0721
Polymers7,0721
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3820 Å2
Unit cell
Length a, b, c (Å)59.023, 36.136, 22.053
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 7071.782 Da / Num. of mol.: 1 / Mutation: T303Q, D347K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19909
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.66 Å3/Da / Density % sol: 26.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MES monohydrate pH 6.5 (buffer system 1), 40% v/v PEG 500* MME, 20 % w/v PEG 20000 (Precipitant mix1) (Morpheus Screen ID 25).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.4→30.82 Å / Num. obs: 2003 / % possible obs: 98 % / Redundancy: 6.3 % / CC1/2: 0.973 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.093 / Rrim(I) all: 0.233 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.41-2.546.30.53917022690.7950.2330.5893.896.7
7.61-30.825.10.127415820.9840.0610.1425.796.5

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1pgb

1pgb


Resolution: 2.4→30.819 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 15.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3047 208 10.44 %RANDOM
Rwork0.2004 1784 --
obs0.2112 1992 97.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.7 Å2 / Biso mean: 33.7382 Å2 / Biso min: 12.19 Å2
Refinement stepCycle: final / Resolution: 2.4→30.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms439 0 0 7 446
Biso mean---36.96 -
Num. residues----56
LS refinement shellResolution: 2.406→30.81 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3047 208 -
Rwork0.2004 1784 -
obs--97 %

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