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- PDB-1fcl: DELTA1.5: A COMPUTATIONALLY DESIGNED CORE VARIANT OF THE B1 DOMAI... -

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Basic information

Entry
Database: PDB / ID: 1fcl
TitleDELTA1.5: A COMPUTATIONALLY DESIGNED CORE VARIANT OF THE B1 DOMAIN OF STREPTOCOCCAL PROTEIN G
ComponentsIMMUNOGLOBULIN G BINDING PROTEIN G
KeywordsPROTEIN BINDING / Designed Core Mutant / Streptococcal Protein G
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / M protein-type anchor domain / Ubiquitin-like (UB roll) - #10 / 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 / M protein-type anchor domain / Ubiquitin-like (UB roll) - #10 / 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. (bacteria)
MethodSOLUTION NMR / Standard Distance Geometry, simulated Annealing Methods
AuthorsRoss, S.A. / Sarisky, C.A. / Su, A. / Mayo, S.L.
CitationJournal: Protein Sci. / Year: 2001
Title: Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification.
Authors: Ross, S.A. / Sarisky, C.A. / Su, A. / Mayo, S.L.
History
DepositionJul 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN G BINDING PROTEIN G


Theoretical massNumber of molelcules
Total (without water)6,2171
Polymers6,2171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100Structures with the Least Restraint Violations, Structures with the Lowest Energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody IMMUNOGLOBULIN G BINDING PROTEIN G / IGG BINDING PROTEIN G


Mass: 6216.819 Da / Num. of mol.: 1 / Fragment: GB1_DELTA1.5 / Mutation: Y3F, L7I, F30L, A34I, V39I, F52W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P19909

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131E-COSY
141TOCSY
NMR detailsText: none

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Sample preparation

DetailsContents: 1 mM unlabeled protein in 50 mM sodium phosphate, pH 6.0
Solvent system: either D2O or 90:10 H2O:D2O
Sample conditionsIonic strength: 50 mM sodium phosphate / pH: 6 / Pressure: Atmospheric atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.2f, 5.3a, 6.1bVariancollection
NMRCompass2.5MSIprocessing
ANSIG3.3P. Kraulisprocessing
X-PLOR3.1Brungerrefinement
RefinementMethod: Standard Distance Geometry, simulated Annealing Methods
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Structures with the Least Restraint Violations, Structures with the Lowest Energy
Conformers calculated total number: 100 / Conformers submitted total number: 40

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