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- PDB-3gb1: STRUCTURES OF B1 DOMAIN OF STREPTOCOCCAL PROTEIN G -

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Basic information

Entry
Database: PDB / ID: 3gb1
TitleSTRUCTURES OF B1 DOMAIN OF STREPTOCOCCAL PROTEIN G
ComponentsPROTEIN (B1 DOMAIN OF STREPTOCOCCAL PROTEIN G)
KeywordsIMMUNOGLOBULIN 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
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. 'group G' (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M.
Citation
Journal: J.Am.Chem.Soc. / Year: 1999
Title: Improving the Packing and Accuracy of NMR Structures with a Pseudopotential for the Radius of Gyration
Authors: Juszewski, K. / Gronenborn, A.M. / Clore, G.M.
#1: Journal: J.Am.Chem.Soc. / Year: 1998
Title: Measurement of Residual Dipolar Couplings of Macromolecules Aligned in the Nematic Phase of a Colloidal Suspension of Rod-Shaped Viruses.
Authors: Clore, G.M. / Starich, M.R. / Gronenborn, A.M.
#2: 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
DepositionMay 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (B1 DOMAIN OF STREPTOCOCCAL PROTEIN G)


Theoretical massNumber of molelcules
Total (without water)6,2021
Polymers6,2021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 32RESTRAINED MINIMIZATION
RepresentativeModel #1

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Components

#1: Protein PROTEIN (B1 DOMAIN OF STREPTOCOCCAL PROTEIN G)


Mass: 6201.784 Da / Num. of mol.: 1 / Fragment: B1 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P06654*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D HOMO AND HETERONUCLEAR
1213D QUNATITATIVE J CORRELATION

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Sample preparation

Sample conditionsPressure: AMBIENT / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AM600 / Manufacturer: Bruker / Model: AM600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS/XPLORBRUNGER, A., CLORE, G.M. ET AL.refinement
CNS/XPLOR MODIFIEDMODIFIEDstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: INCORPORATES RADIUS OF GYRATION RESTRAINT AND DIPOLAR COUPLINGS A TOTAL OF 31 SIMULATED ANNEALING STRUCTURES WERE CALCULATED THE COORDINATES OF THE RESTRAINED MINIMIZED STRUCTURE ARE LISTED ...Details: INCORPORATES RADIUS OF GYRATION RESTRAINT AND DIPOLAR COUPLINGS A TOTAL OF 31 SIMULATED ANNEALING STRUCTURES WERE CALCULATED THE COORDINATES OF THE RESTRAINED MINIMIZED STRUCTURE ARE LISTED FIRST. THIS WAS OBTAINED BY AVERAGING THE COORDINATES OF THE INDIVIDUAL STRUCTURES AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. IN THE CASE OF THE RESTRAINED MINIMIZED MEAN STRUCTURE THE QUANTITY PRESENTED IN THE B VALUE FIELD (COLUMNS 61 - 66 OF THE ATOM AND HETATM RECORDS BELOW) REPRESENTS THE ATOMIC RMS DEVIATION OF THE INDIVIDUAL STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS. FOR THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES THE NUMBERS IN THE B-FACTOR C NO MEANING ALL THE INTERPROTON DISTANCE, TORSION ANGLE RESTRAINTS 3G AND DIPOLAR COUPLING RESTRAINTS ARE AVAILABLE FROM THE PROTEIN DATA BANK AS A SEPARATE ENTRY. (RMR3GB1) TERMS IN TARGET FUNCTION USED FOR SIMULATED ANNEALING: NOE (SUM AVERAGING) AND TORSION ANGLE RESTRAINTS 3JHNALPHA COUPLING CONSTANT RESTRAINTS (GARRETT ET AL J. MAGN. RESON. B104, 99-103 (1994). DIPOLAR COUPLING RESTRAINTS USING TWO ALIGNMENT TENSO (IN TMV AND IN BICELLES) TERM FOR THE RADIUS OF GYRATION (KUSZEWSKI J, GRONENB CLORE, GM J AM CHEM SOC 121, 2337-2338 (1999)) TORSION ANGLE DATABASE POTENTIAL (KUSZEWSKI J, GRONEN CLORE GM. PROTEIN SCI 5, 1067-1080 (1996); J. MAGN 125, 171-177 (1997). COVALENT GEOMETRY RESTRAINTS (BONDS, ANGLES, IMPROPER QUARTIC VAN DER WAALS REPULSION TERM (NILGES. M, GRONENBORN, A.M., BRUNGER, A.T., CLORE, G.M. (1988) PROTEIN ENG. 2, 27-38). RESTRAINTS: NOES: 138 SEQUENTIAL, 133 MEDIUM, 279 LONG RANGE IN 185 INTRARESIDUE TORSION ANGLES: 145 3JHNALPHA COUPLINGS: 53 DIPOLAR COUPLINGS: 152 IN TMV AND 148 IN BICELLES (NH, N-C AND HN-C) THE B-FACTOR COLUMN GIVES THE AVERAGE RMS OF THE 31 SIMULATED AN STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS FILENAME=G_TMV_BICE_RGYR_AVE.MIN ============================================================ BONDS,ANGLES,IMPROPERS,CDIH,NOE,COUP 162664E-03,0.47617,0.436105,0,1.84255E-02,0.534352 ============================================================
NMR ensembleConformer selection criteria: RESTRAINED MINIMIZATION / Conformers calculated total number: 32 / Conformers submitted total number: 32

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