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- PDB-2ka0: NMR structure of the protein TM1367 -

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Basic information

Entry
Database: PDB / ID: 2ka0
TitleNMR structure of the protein TM1367
Componentsuncharacterized protein TM1367
Keywordsstructural genomics / unknown function / TM1367 / Termotoga maritima / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homologyTM1367-like / Cyclophilin TM1367-like domain / Cyclophilin-like / Cyclophilin - #20 / Cyclophilin / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta / Cyclophilin TM1367-like 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 27, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: 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 TM1367


Theoretical massNumber of molelcules
Total (without water)13,9391
Polymers13,9391
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 / 80CYANA TARGET FUNCTION
RepresentativeModel #1closest to the average

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Components

#1: Protein uncharacterized protein TM1367


Mass: 13939.089 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Species: maritima / Gene: TM_1367 / Plasmid: pET25b / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta DE3 / References: UniProt: Q9X187

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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
1313D 15N-resolved [1H,1H]-NOESY
1413D 13C-resolved [1H,1H]-NOESY (aliphatic 13C)
1513D 13C-resolved [1H,1H]-NOESY (aromatic 13C)
1614D-APSY-HACANH
1715D-APSY-(HA)CA(CO)NH
1815D-APSY-CBCA(CO)NH

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Sample preparation

DetailsContents: 1.5 mM [U-98% 13C; U-98% 15N] PROTEIN, 0.5mM DTT, 4.5mM d10-DTT, 0.03% AZIDE, 50 mM SODIUM CHLORIDE, 25 mM SODIUM PHOSPHATE, 10 % D2O, 90 % H2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.5 mMPROTEIN1
0.5 mMDTT1
4.5 mMD10-DTT1
0.03 %sodium azide1
50 mMsodium chloride1
25 mMsodium phosphate1
10 %D2O1
90 %H2O1
Sample conditionsIonic strength: 0.2M / pH: 6.0 / 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
OPALLUGINBUHL, GUNTERT, BILLETER and WUTHRICHrefinement
CYANA3GUNTERT, MUMENTHALER and WUTHRICHstructure solution
ATNOSHERRMANN, GUNTERT and WUTHRICHstructure solution
CANDID2HERRMANN, GUNTERT and WUTHRICHstructure solution
TopSpin1.3BRUKER BIOSPINcollection
CARAKELLER and WUTHRICHdata analysis
ASCAN(ASCAN)-FIORITO, HERRMANN, DAMBERGER and WUTHRICHdata analysis
MATCH(MATCH)-VOLK, HERRMANN and WUTHRICHdata analysis
MOLMOLKORADI, BILLETER 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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