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- PDB-2k75: Solution NMR structure of the OB domain of Ta0387 from Thermoplas... -

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Basic information

Entry
Database: PDB / ID: 2k75
TitleSolution NMR structure of the OB domain of Ta0387 from Thermoplasma acidophilum. Northeast Structural Genomics Consortium target TaR80b.
Componentsuncharacterized protein Ta0387
KeywordsDNA BINDING PROTEIN / closed beta barrel / OB fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / unknown function
Function / homologyNucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesThermoplasma acidophilum (acidophilic)
MethodSOLUTION NMR / simulated annealing
Model detailsOB fold
AuthorsRamelot, T.A. / Ding, K. / Lee, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G. / Acton, T.B. ...Ramelot, T.A. / Ding, K. / Lee, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the OB domain of Ta0387 from Thermoplasma acidophilum.
Authors: Ramelot, T.A. / Ding, K. / Lee, D. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A.
History
DepositionAug 1, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 1.3May 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: uncharacterized protein Ta0387


Theoretical massNumber of molelcules
Total (without water)11,8961
Polymers11,8961
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 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein uncharacterized protein Ta0387


Mass: 11896.184 Da / Num. of mol.: 1 / Fragment: residues 105-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Species: acidophilum / Gene: Ta0387 / Plasmid: pET21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: Q9HL44

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: OB fold
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-13C HSQC
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1613D HNCO
1713D HNCA
1813D HN(CA)CB
1913D CBCA(CO)NH
11013D HBHA(CO)NH
11113D (H)CCH-TOCSY
11213D (H)CCH-COSY
11313D H(CCO)NH
11413D C(CO)NH
11532D 1H-15N HSQC
11632D 1H-13C HSQC
11733D 1H-13C NOESY
11834D CC NOESY
11913D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide, 1.0 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
220 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide, 1.3 mM [U-5% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
320 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide, 1.0 mM [U-100% 13C; U-100% 15N] protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMammonium acetate1
100 mMsodium chloride1
10 mMDTT1
5 mMcalcium chloride1
0.02 %sodium azide1
1.0 mMprotein[U-100% 13C; U-100% 15N]1
20 mMammonium acetate2
100 mMsodium chloride2
10 mMDTT2
5 mMcalcium chloride2
0.02 %sodium azide2
1.3 mMprotein[U-5% 13C; U-100% 15N]2
20 mMammonium acetate3
100 mMsodium chloride3
10 mMDTT3
5 mMcalcium chloride3
0.02 %sodium azide3
1.0 mMprotein[U-100% 13C; U-100% 15N]3
Sample conditionsIonic strength: 100 / pH: 4.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceIIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipelinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.20.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.20.0Schwieters, Kuszewski, Tjandra and Clorerefinement
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Xplor-NIH
NMR constraintsNOE constraints total: 1313 / NOE intraresidue total count: 294 / NOE long range total count: 526 / NOE medium range total count: 133 / NOE sequential total count: 360 / Hydrogen bond constraints total count: 90 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 65 / Protein psi angle constraints total count: 65
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 2.7 ° / Maximum upper distance constraint violation: 0.3 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

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