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- PDB-2gp8: NMR SOLUTION STRUCTURE OF THE COAT PROTEIN-BINDING DOMAIN OF BACT... -

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Basic information

Entry
Database: PDB / ID: 2gp8
TitleNMR SOLUTION STRUCTURE OF THE COAT PROTEIN-BINDING DOMAIN OF BACTERIOPHAGE P22 SCAFFOLDING PROTEIN
ComponentsPROTEIN (SCAFFOLDING PROTEIN)
KeywordsVIRAL PROTEIN / SCAFFOLDING PROTEIN / COAT PROTEIN-BINDING DOMAIN / HELIX-LOOP-HELIX MOTIF
Function / homologyVirus Scaffolding Protein; Chain A / Virus Scaffolding Protein; Chain A / Bacteriophage P22, Gp8, scaffold / Bacteriophage, scaffolding protein / Virus scaffolding protein, C-terminal / Few Secondary Structures / Irregular / Scaffolding protein
Function and homology information
Biological speciesEnterobacteria phage P22 (virus)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
Model type detailsminimized average
AuthorsSun, Y. / Parker, M.H. / Weigele, P. / Casjens, S. / Prevelige Jr., P.E. / Krishna, N.R.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structure of the coat protein-binding domain of the scaffolding protein from a double-stranded DNA virus.
Authors: Sun, Y. / Parker, M.H. / Weigele, P. / Casjens, S. / Prevelige Jr., P.E. / Krishna, N.R.
History
DepositionMay 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 17, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (SCAFFOLDING PROTEIN)


Theoretical massNumber of molelcules
Total (without water)4,3291
Polymers4,3291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100LEAST RESTRAINT VIOLATION
Representativeminimized average structure

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Components

#1: Protein/peptide PROTEIN (SCAFFOLDING PROTEIN)


Mass: 4329.034 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FUNCTIONAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): NF1829 / References: UniProt: P26748

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
14115N EDITED 3D NOESY-HSQC
151TOCSYHMQC
NMR detailsText: AVERAGE STRUCTURE. EXPERIMENTS WERE DONE ON THE C-TERMINAL 67-RESIDUE (238-303 PLUS ALANINE AT THE N-TERNINUS) SCAFFOLDING PROTEIN.

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Sample preparation

DetailsContents: 10% WATER/90% D2O, 99.9% D2O
Sample conditionspH: 4.4 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AM600BrukerAM6006001
Varian AVANCE600VarianAVANCE6006002
Varian INOVA600VarianINOVA6006003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE REFINEMENT WAS CARRIED OUT ON THE C-TERMINAL 40-RESIDUE SEGMENT.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 1

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