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- PDB-1rdu: NMR STRUCTURE OF A PUTATIVE NIFB PROTEIN FROM THERMOTOGA (TM1290)... -

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Basic information

Entry
Database: PDB / ID: 1rdu
TitleNMR STRUCTURE OF A PUTATIVE NIFB PROTEIN FROM THERMOTOGA (TM1290), WHICH BELONGS TO THE DUF35 FAMILY
Componentsconserved hypothetical protein
KeywordsBIOSYNTHETIC PROTEIN / ATNOS / CANDID / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Nitrogen fixation NifB
Function / homologyMTH1175 domain / Dinitrogenase iron-molybdenum cofactor biosynthesis domain / Dinitrogenase iron-molybdenum cofactor biosynthesis / Dinitrogenase iron-molybdenum cofactor biosynthesis superfamily / Dinitrogenase iron-molybdenum cofactor / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / Dinitrogenase iron-molybdenum cofactor biosynthesis domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsEtezady-Esfarjani, T. / Herrmann, T. / Peti, W. / Klock, H.E. / Lesley, S.A. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: J.Biomol.NMR / Year: 2004
Title: NMR Structure Determination of the Hypothetical Protein TM1290 from Thermotoga Maritima using Automated NOESY Analysis.
Authors: Etezady-Esfarjani, T. / Herrmann, T. / Peti, W. / Klock, H.E. / Lesley, S.A. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
History
DepositionNov 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: 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: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)12,5511
Polymers12,5511
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)20 / 80target function
RepresentativeModel #2closest to the average

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Components

#1: Protein conserved hypothetical protein


Mass: 12551.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm1290 / Plasmid: pET25B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9X116

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2223D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
12.3mM 15N-labeled TM1290, 95% H2O/5% D2O, 20mM sodium phosphate, pH 6.095% H2O/5% D2O, 20mM sodium phosphate, pH 6.0
23.8mM 15N-13C-labeled TM1290, 95% H2O/5% D2O, 20mM sodium phosphate, pH 6.095% H2O/5% D2O, 20mM sodium phosphate, pH 6.0
Sample conditions
Conditions-IDpHTemperature (K)
16313 K
26313 K

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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
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA6Guentertrefinement
XwinNMR3.5data analysis
XEASYdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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