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- PDB-1pgx: THE 1.66 ANGSTROMS X-RAY STRUCTURE OF THE B2 IMMUNOGLOBULIN-BINDI... -

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Basic information

Entry
Database: PDB / ID: 1pgx
TitleTHE 1.66 ANGSTROMS X-RAY STRUCTURE OF THE B2 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON TO THE NMR STRUCTURE OF THE B1 DOMAIN
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 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.66 Å
AuthorsWhitlow, M. / Achari, A. / Howard, A.J.
Citation
Journal: Biochemistry / Year: 1992
Title: 1.67-A 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.
#1: 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.
#2: Journal: Bacterial Immunoglobulin-Binding Proteins / Year: 1990
Title: Structure and Evolution of the Streptococcal Genes Encoding Protein G
Authors: Fahnestock, S.R. / Alexander, P. / Filpula, D. / Nagle, J.
History
DepositionApr 3, 1992Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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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)9,0161
Polymers9,0161
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.040, 34.500, 35.950
Angle α, β, γ (deg.)90.00, 100.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN G


Mass: 9015.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus (bacteria) / Genus: Streptococcus / References: UniProt: P06654
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.76 Å3/Da / Density % sol: 30.08 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mMsodium citrate1drop
210 mMCaCl21drop
310 %PEG-33501drop
410 mMoctyl beta-glucoside1drop
517.5 mg/mlprotein1drop
625 %PEG-33501reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.66 Å / Rmerge F obs: 0.0327

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.66→8 Å /
RfactorNum. reflection
obs0.191 6365
Refinement stepCycle: LAST / Resolution: 1.66→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms536 0 0 63 599
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.03
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
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_restr0.0180.03
X-RAY DIFFRACTIONp_chiral_restr0.210.3
X-RAY DIFFRACTIONp_singtor_nbd0.1640.2
X-RAY DIFFRACTIONp_multtor_nbd0.1410.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1330.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.26
X-RAY DIFFRACTIONp_staggered_tor13.510
X-RAY DIFFRACTIONp_orthonormal_tor22.210
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.66 Å / Lowest resolution: 8 Å / Num. reflection obs: 6365 / σ(F): 2 / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18 Å2

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