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- PDB-1de1: NMR STRUCTURES OF OXIDIZED BACTERIOPHAGE T4 GLUTAREDOXIN -

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Basic information

Entry
Database: PDB / ID: 1de1
TitleNMR STRUCTURES OF OXIDIZED BACTERIOPHAGE T4 GLUTAREDOXIN
ComponentsGLUTAREDOXIN
KeywordsELECTRON TRANSPORT / GLUTAREDOXIN
Function / homology
Function and homology information


deoxyribonucleotide biosynthetic process
Similarity search - Function
Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS
AuthorsWang, Y. / Amegbey, G. / Wishart, D.S.
CitationJournal: J.Biomol.Nmr / Year: 2004
Title: Solution structures of reduced and oxidized bacteriophage T4 glutaredoxin.
Authors: Wang, Y. / Amegbey, G. / Wishart, D.S.
History
DepositionNov 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAREDOXIN


Theoretical massNumber of molelcules
Total (without water)10,0641
Polymers10,0641
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)30 / 50BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM,STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION
RepresentativeModel #24closest to the average

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Components

#1: Protein GLUTAREDOXIN


Mass: 10063.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: THIS SEQUENCE OCCURS NATURALLY IN BACTERIOPHAGE T4 / Source: (natural) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / References: UniProt: P00276
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY, TOCSY, DQF COSY
NMR detailsText: THE STRUCTURES WERE DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

DetailsContents: 2MM T4 GLUTAREDOXIN; 50MM PH7.0 PHOSPHATE BUFFER
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: AMBIENT / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1VARIANdata analysis
X-PLOR3.85BRUNGER, A. T.structure solution
X-PLOR3.85BRUNGER, A. T.refinement
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON 1050 DISTANCE, 188 DIHEDRAL ANGLE AND 201 H CHEMICAL SHIFT CONSTRAINTS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM,STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY, STRUCTURES WITH THE ...Conformer selection criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM,STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION
Conformers calculated total number: 50 / Conformers submitted total number: 30

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