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- PDB-4wh4: Protein GB1 Quadruple Mutant I6H/N8H/K28H/Q32H -

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Basic information

Entry
Database: PDB / ID: 4wh4
TitleProtein GB1 Quadruple Mutant I6H/N8H/K28H/Q32H
ComponentsImmunoglobulin G-binding protein G
KeywordsSIGNALING PROTEIN / Immunoglobulin-Binding Domain
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 / Ubiquitin-like (UB roll) - #10 / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / 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 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCunningham, T.C. / Horne, W.S. / Saxena, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1157712 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: The double-histidine Cu2+-binding motif: a highly rigid, site-specific spin probe for electron spin resonance distance measurements.
Authors: Cunningham, T.F. / Putterman, M.R. / Desai, A. / Horne, W.S. / Saxena, S.
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G
B: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1508
Polymers12,5942
Non-polymers5576
Water52229
1
A: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6695
Polymers6,2971
Non-polymers3724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4813
Polymers6,2971
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.287, 74.287, 41.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 6296.827 Da / Num. of mol.: 2 / Mutation: I6H/N8H/K28H/Q32H
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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.75 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 5, 2014
RadiationMonochromator: Rigaku VariMax Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→32.17 Å / Num. obs: 6876 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1690) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QMT

2qmt


Resolution: 2.2→32.167 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2559 697 10.19 %
Rwork0.2013 --
obs0.2068 6837 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→32.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms888 0 35 29 952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004937
X-RAY DIFFRACTIONf_angle_d0.6471265
X-RAY DIFFRACTIONf_dihedral_angle_d13.947318
X-RAY DIFFRACTIONf_chiral_restr0.023138
X-RAY DIFFRACTIONf_plane_restr0.002158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.36980.33511350.26471200X-RAY DIFFRACTION98
2.3698-2.60820.29231390.25361191X-RAY DIFFRACTION99
2.6082-2.98540.3181350.25351223X-RAY DIFFRACTION99
2.9854-3.76040.28341370.19731245X-RAY DIFFRACTION100
3.7604-32.17090.20391510.16871281X-RAY DIFFRACTION100

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