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- PDB-9i2i: X-ray structure of the B1 domain of streptococcal protein G tripl... -

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Basic information

Entry
Database: PDB / ID: 9i2i
TitleX-ray structure of the B1 domain of streptococcal protein G triple mutant T2Q, N8D, and N37D (GB1-QDD).
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / GB1 / crystallographic dimer
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. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsEngilberge, S. / Becker, L.M. / Kapitonova, A. / Schanda, P.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Biorxiv / Year: 2025
Title: Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes
Authors: Becker, L.M. / Fu, H. / Tatman, B.P. / Dreydoppel, M. / Kapitonova, A. / Weininger, U. / Engilberge, S. / Chipot, C. / Schanda, P.
History
DepositionJan 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Data collection / Category: diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list

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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)12,4853
Polymers12,4622
Non-polymers231
Water2,648147
1
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2311
Polymers6,2311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunoglobulin G-binding protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2542
Polymers6,2311
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.480, 35.186, 49.943
Angle α, β, γ (deg.)90.000, 122.512, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 6230.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / References: UniProt: P19909
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 278 K / Method: microdialysis / Details: 50% MPD, 25% isopropyl alcohol,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.08→42.11 Å / Num. obs: 43133 / % possible obs: 96.6 % / Redundancy: 13.5 % / Biso Wilson estimate: 16.15 Å2 / CC1/2: 0.989 / Rpim(I) all: 0.012 / Net I/σ(I): 22.6
Reflection shellResolution: 1.08→1.21 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1250 / CC1/2: 0.87 / Rpim(I) all: 0.259

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→20.82 Å / SU ML: 0.1337 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 42.6858
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2096 1242 4.97 %
Rwork0.18 23762 -
obs0.1815 25004 51.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.88 Å2
Refinement stepCycle: LAST / Resolution: 1.08→20.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms853 0 1 147 1001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077922
X-RAY DIFFRACTIONf_angle_d0.99551259
X-RAY DIFFRACTIONf_chiral_restr0.068149
X-RAY DIFFRACTIONf_plane_restr0.0106161
X-RAY DIFFRACTIONf_dihedral_angle_d13.123339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.120.2461100.383582X-RAY DIFFRACTION1.71
1.12-1.180.1521200.2782418X-RAY DIFFRACTION8.17
1.18-1.240.2978530.24541063X-RAY DIFFRACTION20.91
1.24-1.310.2481750.24891705X-RAY DIFFRACTION33
1.31-1.420.30251170.24772411X-RAY DIFFRACTION46.84
1.42-1.560.25921810.2123286X-RAY DIFFRACTION64.25
1.56-1.780.23242440.2064456X-RAY DIFFRACTION86.75
1.78-2.250.22212500.18095112X-RAY DIFFRACTION98.6
2.25-20.820.19242920.16665229X-RAY DIFFRACTION99.71

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