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- PDB-1igd: THE THIRD IGG-BINDING DOMAIN FROM STREPTOCOCCAL PROTEIN G: AN ANA... -

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Basic information

Entry
Database: PDB / ID: 1igd
TitleTHE THIRD IGG-BINDING DOMAIN FROM STREPTOCOCCAL PROTEIN G: AN ANALYSIS BY X-RAY CRYSTALLOGRAPHY OF THE STRUCTURE ALONE AND IN A COMPLEX WITH FAB
ComponentsPROTEIN G
KeywordsIMMUNOGLOBULIN BINDING PROTEIN
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / 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. ...IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / 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 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. G148 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.1 Å
AuthorsDerrick, J.P. / Wigley, D.B.
Citation
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.
#1: Journal: Biochemistry / Year: 1994
Title: Two Crystal Structures of the B1 Immunoglobulin-Binding Domain of Streptococcal Protein G and Comparison with NMR
Authors: Gallagher, T. / Alexander, P. / Bryan, P. / Gilliland, G.L.
#2: Journal: Nature / Year: 1992
Title: Crystal Structure of a Streptococcal Protein G Domain Bound to an Fab Fragment
Authors: Derrick, J.P. / Wigley, D.B.
#3: Journal: Biochemistry / Year: 1992
Title: 1.67 Angstroms X-Ray Structure of the B2 Immunoglobulin-Binding Domain of Streptococcal Protein G and Comparison to the NMR Structure of the B1 Domain
Authors: Achari, A. / Hale, S.P. / Howard, A.J. / Clore, G.M. / Gronenborn, A.M. / Hardman, K.D. / Whitlow, M.
#4: Journal: J.Mol.Biol. / Year: 1992
Title: Determination of the Solution Structures of Domains II and III of Protein G from Streptococcus by 1H Nuclear Magnetic Resonance
Authors: Lian, L.Y. / Derrick, J.P. / Sutcliffe, M.J. / Yang, J.C. / Roberts, G.C.K.
#5: Journal: Science / Year: 1991
Title: A Novel, Highly Stable Fold of the Immunoglobulin Binding Domain of Streptococcal Protein G
Authors: Gronenborn, A.M. / Filpula, D.R. / Essig, N.Z. / Achari, A. / Whitlow, M. / Wingfield, P.T. / Clore, G.M.
History
DepositionAug 5, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN G


Theoretical massNumber of molelcules
Total (without water)6,6571
Polymers6,6571
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.900, 40.300, 42.200
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. G148 (bacteria) / Plasmid: PUC18 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P06654
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal grow
*PLUS
pH: 4.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
310 mMsodium acetate1reservoir
40.01 %(w/v)sodium azide1reservoir
524-26 %(w/v)PEG40001reservoir
2reservoir solution1drop0.01 ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 23530 / % possible obs: 95 %
Reflection
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 25 Å / Rmerge(I) obs: 0.058

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.1→25 Å / Rfactor obs: 0.193
Displacement parametersBiso mean: 17.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.05 Å
Refinement stepCycle: LAST / Resolution: 1.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms468 0 0 120 588
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1050.12
X-RAY DIFFRACTIONp_singtor_nbd0.170.5
X-RAY DIFFRACTIONp_multtor_nbd0.20.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2680.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.085
X-RAY DIFFRACTIONp_staggered_tor17.9615
X-RAY DIFFRACTIONp_orthonormal_tor26.1520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ/X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS

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