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- PDB-2k9z: NMR structure of the protein TM1112 -

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Basic information

Entry
Database: PDB / ID: 2k9z
TitleNMR structure of the protein TM1112
Componentsuncharacterized protein TM1112
Keywordsstructural genomics / unknown function / Thermotoga Maritima / TM1112 / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
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 / TORSION ANGLE DYNAMICS, ENERGY MINIMIZATION
AuthorsMohanty, B. / Pedrini, B. / Serrano, P. / Geralt, M. / Horst, R. / Herrmann, T. / Wilson, I.A. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
Authors: Mohanty, B. / Serrano, P. / Pedrini, B. / Jaudzems, K. / Geralt, M. / Horst, R. / Herrmann, T. / Elsliger, M.A. / Wilson, I.A. / Wuthrich, K.
History
DepositionOct 28, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein TM1112


Theoretical massNumber of molelcules
Total (without water)10,7741
Polymers10,7741
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 / 80CYANA TARGET FUNCTION
RepresentativeModel #1closest to the average

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Components

#1: Protein uncharacterized protein TM1112


Mass: 10774.417 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Species: maritima / Gene: TM_1112 / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta DE3 / References: UniProt: Q9X0J6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D [15N,1H]-HSQC
1212D [13C,1H]-HSQC
1314D-APSY-HACANH
1415D-APSY-(HA)CA(CO)NH
1515D-APSY-CBCA(CO)NH
1613D 15N-RESOLVED [1H,1H]-NOESY
1713D 13C-RESOLVED [1H,1H]-NOESY (ALIPHATIC 13C)
1813D 13C-RESOLVED [1H,1H]-NOESY (AROMATIC 13C)

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Sample preparation

DetailsContents: 1.3 mM [U-98% 13C; U-98% 15N] TM1112, 0.5mM DTT, 4.5 mM D10-DTT, 25 mM potassium phosphate, 50 mM sodium chloride, 0.03 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMTM1112[U-98% 13C; U-98% 15N]1
0.5 mMDTT1
4.5 mMD10-DTT1
25 mMpotassium phosphate1
50 mMsodium chloride1
0.03 %sodium azide1
Sample conditionsIonic strength: 0.2M / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
ATNOSHerrmann, Guntert and Wuthrichstructure solution
CANDID2Herrmann, Guntert and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
ASCANASCAN Fiorito, Herrmann, Damberger and Wuthrichdata analysis
CARAKeller and Wuthrichdata analysis
TopSpin1.3Bruker Biospindata analysis
TopSpin1.3Bruker Biospindata analysis
MATCHVolk, Herrmann and Wuthrichdata analysis
RefinementMethod: TORSION ANGLE DYNAMICS, ENERGY MINIMIZATION / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: CYANA TARGET FUNCTION / Conformers calculated total number: 80 / Conformers submitted total number: 20

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