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- PDB-1rwd: Backbone NMR Structure of a Mutant P. Furiosus Rubredoxin Using R... -

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Basic information

Entry
Database: PDB / ID: 1rwd
TitleBackbone NMR Structure of a Mutant P. Furiosus Rubredoxin Using Residual Dipolar Couplings
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / residual dipolar couplings / structural genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


electron transfer activity / iron ion binding
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 speciesPyrococcus furiosus (archaea)
MethodSOLUTION NMR / RDC directed fragment assembly
AuthorsTian, F. / Valafar, H. / Prestegard, J.H. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: J.Am.Chem.Soc. / Year: 2001
Title: A Dipolar Coupling Based Strategy for Simultaneous Resonance Assignment and Structure Determination of Protein Backbones
Authors: Tian, F. / Valafar, H. / Prestegard, J.H.
History
DepositionDec 16, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionDec 23, 2003ID: 1M2Y
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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

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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)5,8631
Polymers5,8631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1fewest violations

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Components

#1: Protein Rubredoxin / / Rd


Mass: 5863.470 Da / Num. of mol.: 1 / Mutation: W3Y, I23V, L32I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: RUB, PF1282 / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / Strain (production host): NCM533 / References: UniProt: P24297

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111soft HNCA-E.COSY
121modified HNCO
131phase-MODULATED HSQC
242soft HNCA-E.COSY
252modified HNCO
262phase-MODULATED HSQC
173soft HNCA-E.COSY
183modified HNCO
193phase-MODULATED HSQC
NMR detailsText: Structure was determined using residual dipolar couplings from backbone atom pairs; modeled as an Ala-Gly polypeptide

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Sample preparation

Details
Solution-IDContentsSolvent system
14.5 mM Rubredoxin U-15N; 50 mM Na Phosphate; 100 mM NaCl; pH 6.390% H2O/10% D2O
22.5 mM Rubredoxin U-15N; 50 mM Na Phosphate ; 50 mM NaCl; pH 6.3; 7% Bicelle (3:1 DMPC:DHPC with 4% CTAB relative to DMPC)Bicelles in 90% H2O, 10% D2O
34.5 mM Rubredoxin U-15N; 50 mM Na Phosphate; 100 mM NaCl; pH 6.3; PF1 phage samplePhage in 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 6.3 ambient 298 K
250 mM NaCl 6.3 ambient 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
REDcRAFT1Valafar, H. & Prestegard, J.H.structure solution
XPLOR-NIH2.9.1Schwieters, C.D., Kuszewski, J.J., Tjandra, N. & Clore, G.M.refinement
REDCAT1Valafar, H. & Prestegard, J.H.data analysis
RefinementMethod: RDC directed fragment assembly / Software ordinal: 1
Details: RDCs were used in the initial assembly of 6 fragments. RDCs from two media were used to set relative orientation of fragments. Translational relationships of fragments were dictated by ...Details: RDCs were used in the initial assembly of 6 fragments. RDCs from two media were used to set relative orientation of fragments. Translational relationships of fragments were dictated by sequence connectivities. The assembled structure was minimized using a molecular force field and RDC error function. All sidechain atoms beyond CB are missing.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformers submitted total number: 1

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