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- PDB-1t3v: The NMR solution structure of TM1816 -

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Basic information

Entry
Database: PDB / ID: 1t3v
TitleThe NMR solution structure of TM1816
Componentsconserved hypothetical protein
KeywordsStructural Genomics / UNKNOWN FUNCTION / alpha-beta / Protein Structure Initiative / PSI / Joint Center for Structural Genomics / JCSG
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
AuthorsColumbus, L. / Peti, W. / Herrmann, T. / Etazady, T. / Klock, H. / Lesley, S. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2005
Title: NMR structure determination of the conserved hypothetical protein TM1816 from Thermotoga maritima.
Authors: Columbus, L. / Peti, W. / Etezady-Esfarjani, T. / Herrmann, T. / Wuthrich, K.
History
DepositionApr 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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)13,6481
Polymers13,6481
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)22 / 80lowest target function
RepresentativeModel #1closest to the average

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Components

#1: Protein conserved hypothetical protein


Mass: 13648.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1816 / Plasmid: pET-25b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL(DE3) / References: UniProt: Q9X2D6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 2 mM TM1816 U-15N,13C; 20mM phosphate buffer / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20 mM sodium phpshate / pH: 6 / Pressure: ambient / Temperature: 313 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 DRXBrukerDRX8002

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Processing

NMR software
NameClassification
Amberrefinement
DYANAstructure solution
XwinNMRcollection
XEASYdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: lowest target function / Conformers calculated total number: 80 / Conformers submitted total number: 22

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