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- PDB-1e8j: SOLUTION STRUCTURE OF DESULFOVIBRIO GIGAS ZINC RUBREDOXIN, NMR, 2... -

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Basic information

Entry
Database: PDB / ID: 1e8j
TitleSOLUTION STRUCTURE OF DESULFOVIBRIO GIGAS ZINC RUBREDOXIN, NMR, 20 STRUCTURES
ComponentsRUBREDOXIN
KeywordsELECTRON TRANSPORT / ZINC-SUBSTITUTION / THERMOSTABILITY
Function / homology
Function and homology information


electron transfer activity / iron ion binding / cytoplasm
Similarity search - Function
Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesDESULFOVIBRIO GIGAS (bacteria)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING
AuthorsLamosa, P. / Brennan, L. / Vis, H. / Turner, D.L. / Santos, H.
Citation
Journal: Extremophiles / Year: 2001
Title: NMR structure of Desulfovibrio gigas rubredoxin: a model for studying protein stabilization by compatible solutes.
Authors: Lamosa, P. / Brennan, L. / Vis, H. / Turner, D.L. / Santos, H.
#1: Journal: Appl.Environ.Microbiol. / Year: 2000
Title: Thermostabilization of Proteins by Diglycerol Phosphate, a New Compatible Solute from the Hyperthermophile Archaeoglobus Fulgidus
Authors: Lamosa, P. / Burke, A. / Peist, R. / Huber, R. / Liu, M.-Y. / Silva, G. / Rodrigues-Pousada, C. / Legall, J. / Maycock, C. / Santos, H.
History
DepositionSep 21, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2001Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.page_last / _citation.title / _pdbx_database_status.status_code_mr

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RUBREDOXIN


Theoretical massNumber of molelcules
Total (without water)5,6821
Polymers5,6821
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein RUBREDOXIN /


Mass: 5682.304 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: IRON-SULFUR-PROTEIN, ZINC SUBSTITUTED / Source: (gene. exp.) DESULFOVIBRIO GIGAS (bacteria) / Cellular location: CYTOPLASM / Plasmid: PRPPL1 / Cellular location (production host): CYTOPLASM / Gene (production host): RDDG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P00270

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D-1H-NOESY 2D-1H-TOCSY 2D-1H-COSY

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Sample preparation

Sample conditionspH: 7.6 / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
INDYANAD.L.TURNER,L.BRENNAN,H. MEYER,C.LOHAUS, C.SIETHOFF,H.S.COSTA,B.GONZALEZ,H.SANTOS, J.E.SUAREZrefinement
INDYANAstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 500 / Conformers submitted total number: 20

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