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- PDB-6kmc: Crystal structure of a Streptococcal protein G B1 mutant -

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Basic information

Entry
Database: PDB / ID: 6kmc
TitleCrystal structure of a Streptococcal protein G B1 mutant
ComponentsImmunoglobulin G-binding protein G B1
KeywordsIMMUNE SYSTEM / Streptococcal protein G B1 Domain / Immunoglobulin binding 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 / 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
ACETIC ACID / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. 'group G' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsWatanabe, H. / Honda, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)18K04860 Japan
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Histidine-Mediated Intramolecular Electrostatic Repulsion for Controlling pH-Dependent Protein-Protein Interaction.
Authors: Watanabe, H. / Yoshida, C. / Ooishi, A. / Nakai, Y. / Ueda, M. / Isobe, Y. / Honda, S.
History
DepositionJul 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G B1
B: Immunoglobulin G-binding protein G B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0083
Polymers12,9482
Non-polymers601
Water1,982110
1
A: Immunoglobulin G-binding protein G B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5342
Polymers6,4741
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunoglobulin G-binding protein G B1


Theoretical massNumber of molelcules
Total (without water)6,4741
Polymers6,4741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.827, 29.439, 36.017
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-250-

HOH

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Components

#1: Antibody Immunoglobulin G-binding protein G B1


Mass: 6474.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19909*PLUS
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.76 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% polyethylene glycol 8000, 100 mM imidazole hydrochloride (pH 8.0), 200 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 12052 / % possible obs: 98.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Χ2: 0.859 / Net I/σ(I): 11.1 / Num. measured all: 75501
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.62-1.655.50.135600.990.060.1440.57693.2
1.65-1.686.30.1215420.9910.0520.1330.58194.9
1.68-1.716.40.1135800.9940.0480.1240.65196.3
1.71-1.756.40.15750.9940.0430.1090.68897.1
1.75-1.786.50.0915920.9950.0390.0990.71199
1.78-1.826.40.0835780.9960.0350.090.67599.1
1.82-1.876.50.0776140.9960.0330.0840.8299.4
1.87-1.926.50.0765770.9960.0320.0820.89899.5
1.92-1.986.10.0676090.9970.030.0730.96999.5
1.98-2.045.90.0645880.9960.0280.070.99799.7
2.04-2.116.30.0586370.9980.0250.0630.95799.7
2.11-2.26.70.0565710.9980.0230.0610.9299.7
2.2-2.36.60.0536070.9980.0220.0580.90699.7
2.3-2.426.60.0526070.9960.0220.0570.95799.7
2.42-2.576.50.0476160.9980.020.0510.93299.8
2.57-2.7760.0466100.9980.020.050.931100
2.77-3.055.80.0426190.9980.0190.0470.915100
3.05-3.496.60.046270.9990.0160.0430.979100
3.49-4.46.30.046390.9990.0170.0431.08499.7
4.4-505.60.047040.9970.0180.0440.913100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZW1

2zw1


Resolution: 1.84→42.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.123 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.179
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 404 4.8 %RANDOM
Rwork0.1973 ---
obs0.2007 7988 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 52.21 Å2 / Biso mean: 18.252 Å2 / Biso min: 4.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2---0.1 Å20 Å2
3---1.19 Å2
Refinement stepCycle: final / Resolution: 1.84→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 4 110 1028
Biso mean--15.79 26.61 -
Num. residues----114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.021941
X-RAY DIFFRACTIONr_angle_refined_deg2.3151.9141277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9455112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7632544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81615154
X-RAY DIFFRACTIONr_chiral_restr0.1590.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02712
LS refinement shellResolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 25 -
Rwork0.226 563 -
all-588 -
obs--99.49 %

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