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- PDB-2igd: ANISOTROPIC STRUCTURE OF PROTEIN G IGG-BINDING DOMAIN III AT 1.1 ... -

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Basic information

Entry
Database: PDB / ID: 2igd
TitleANISOTROPIC STRUCTURE OF PROTEIN G IGG-BINDING DOMAIN III AT 1.1 ANGSTROM RESOLUTION
ComponentsPROTEIN G
KeywordsIGG-BINDING PROTEIN / ATOMIC RESOLUTION / PROTEIN G / IMMUNOGLOBULIN-BINDING / TRANSMEMBRANE
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. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / INITIAL MODEL WAS PREVIOUSLY OBTAINED STRUCTURE / Resolution: 1.1 Å
AuthorsButterworth, S. / Lamzin, V.L. / Wigley, D.B. / Derrick, J.P. / Wilson, K.S.
Citation
Journal: To be Published
Title: Anisotropic Refinement of a Protein G Domain at 1.1 Angstrom Resolution
Authors: Butterworth, S. / Lamzin, V.S. / Wigley, D.B. / Derrick, J.P. / Wilson, K.S.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: The Third Igg-Binding Domain from Streptococcal Protein G. An Analysis by X-Ray Crystallography of the Structure Alone and in a Complex with Fab
Authors: Derrick, J.P. / Wigley, D.B.
History
DepositionApr 30, 1997Processing site: BNL
Revision 1.0Jul 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN G


Theoretical massNumber of molelcules
Total (without water)6,6571
Polymers6,6571
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.050, 40.500, 42.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN G /


Mass: 6657.354 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN-BINDING DOMAIN III
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. (bacteria) / Strain: G148 / Gene: POTENTIAL / Production host: Escherichia coli (E. coli) / Strain (production host): K12 JM101 / References: UniProt: P06654
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.23 Å3/Da / Density % sol: 45 %
Description: EXTENSION OF FORMER ISOTROPIC MODEL TO ANISOTROPIC MODEL
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.8
Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOUR DIFFUSION FROM 24-26% PEG 4000, 10MM SODIUM ACETATE AT PH 4.8 AND 0.01% SODIUM AZIDE. CELL PARAMETERS ARE NOT THOSE DETERMINED EXPERIMENTALLY. THEY ...Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOUR DIFFUSION FROM 24-26% PEG 4000, 10MM SODIUM ACETATE AT PH 4.8 AND 0.01% SODIUM AZIDE. CELL PARAMETERS ARE NOT THOSE DETERMINED EXPERIMENTALLY. THEY WERE ADJUSTED ON THE BASIS OF THE ENGH & HUBER DICTIONARY AT THE END OF REFINEMENT. THE EXPERIMENTAL ESTIMATES WERE KNOWN TO HAVE POTENTIAL ERRORS DUE TO INACCURACIES IN THE CRYSTAL-TO-DETECTOR AND WAVELENGTH CALIBRATION., vapor diffusion - hanging drop

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.72
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1992 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72 Å / Relative weight: 1
ReflectionResolution: 1.1→10.1 Å / Num. obs: 24145 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 39
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 12 / Rsym value: 0.104 / % possible all: 98.1

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Processing

Software
NameClassification
SHELXL-96model building
SHELXL-96refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-96phasing
RefinementMethod to determine structure: INITIAL MODEL WAS PREVIOUSLY OBTAINED STRUCTURE
Starting model: PDB ENTRY 1IGD

1igd


Resolution: 1.1→10 Å / Num. parameters: 5485 / Num. restraintsaints: 6708 / Cross valid method: FREE R-VALUE / Stereochemistry target values: ENGH & HUBER
Details: PROLSQ AND SHELX-93 ALSO USED IN PRELIMINARY STAGES. SHELX-93 AND SHELX-96 REFINEMENT IS AGAINST INTENSITIES.
RfactorNum. reflection% reflectionSelection details
Rfree0.125 1233 5 %5%, RANDOMLY
all0.097 24145 --
obs0.097 -97.9 %-
Solvent computationSolvent model: SHELX-96
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 409.9 / Occupancy sum non hydrogen: 571.7
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms468 0 0 106 574
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.371
X-RAY DIFFRACTIONs_zero_chiral_vol0.115
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.139
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.117

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