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- PDB-1lkn: Solution NMR Structure of Protein TM_1112 from Thermotoga maritim... -

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Basic information

Entry
Database: PDB / ID: 1lkn
TitleSolution NMR Structure of Protein TM_1112 from Thermotoga maritima. Ontario Centre for Structural Proteomics Target TM1112_1_89; Northeast Structural Genomics Consortium Target VT74.
Componentshypothetical protein tm1112
Keywordsstructural genomics / unknown function / BETA BARREL / OCSP / NESG / PROTEIN STRUCTURE INITIATIVE / PSI / Northeast Structural Genomics Consortium
Function / homology(S)-ureidoglycine aminohydrolase, cupin domain / EutQ-like cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / (S)-ureidoglycine aminohydrolase cupin domain-containing protein
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsXia, Y. / Yee, A. / Semesi, A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: to be published
Title: Solution Structure of Hypothetical Protein tm1112
Authors: Xia, Y. / Yee, A. / Semesi, A. / Arrowsmith, C.H.
History
DepositionApr 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: hypothetical protein tm1112


Theoretical massNumber of molelcules
Total (without water)10,7741
Polymers10,7741
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)10 / 30all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein hypothetical protein tm1112


Mass: 10774.417 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm1112 / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): bl21de3(magic gold) / References: UniProt: Q9X0J6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C/15N-separated NOESY
1213D 15N/15N-separated NOESY
131HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 1mM tm1112 U-15N,13C; 25mM phosphate buffer NA; 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 20uM Zn2+ / pH: 6.5 / Pressure: ambient / Temperature: 298 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
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1F. Delaglioprocessing
SparkySPARKY 3T. D. Goddard and D. G. Knellerdata analysis
ARIA BASED ON XPLOR3.851M. NILGES, A.T. Brungerstructure solution
ARIA BASED ON XPLOR3.851M. NILGES, A.T. Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2619 restraints, in which 2508 are NOE-derived distance constraints, 111 are dihedral angle restraints from TALOS analysis and HNHA experiment.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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