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- PDB-1fd6: DELTA0: A COMPUTATIONALLY DESIGNED CORE VARIANT OF THE B1 DOMAIN ... -

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Basic information

Entry
Database: PDB / ID: 1fd6
TitleDELTA0: A COMPUTATIONALLY DESIGNED CORE VARIANT OF THE B1 DOMAIN OF STREPTOCOCCAL PROTEIN G
ComponentsIMMUNOGLOBULIN G BINDING PROTEIN G
KeywordsPROTEIN BINDING / Streptococcal Protein G / Protein Design / Backbone Design / Core Sidechain Packing
Function / homology
Function and homology information


IgG binding / cell wall / : / 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 ...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)
MethodSOLUTION NMR / Distance Geometry, Simulated Annealing
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 19, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IMMUNOGLOBULIN G BINDING PROTEIN G


Theoretical massNumber of molelcules
Total (without water)6,3011
Polymers6,3011
Non-polymers00
Water0
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: 6300.914 Da / Num. of mol.: 1 / Fragment: GB1_DELT0 / Mutation: Y3F, L7I, V39I
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

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Sample preparation

DetailsContents: 3 mM 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: 6.0 / Pressure: ambient / 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, 5.3b, 6.1bVarian Associatescollection
ANSIG3.3P. Kraulisprocessing
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: Distance Geometry, Simulated Annealing / 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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