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- PDB-2kbn: Solution NMR structure of the OB domain (residues 67-166) of MM02... -

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Basic information

Entry
Database: PDB / ID: 2kbn
TitleSolution NMR structure of the OB domain (residues 67-166) of MM0293 from Methanosarcina mazei. Northeast Structural Genomics Consortium target MaR214a.
ComponentsConserved protein
Keywordsstructural genomics / unknown function / nucleic acid binding protein / beta barrel / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyresponse to ionizing radiation / Nucleic acid-binding proteins / double-strand break repair via homologous recombination / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / DNA binding / Mainly Beta / Conserved protein
Function and homology information
Biological speciesMethanosarcina mazei (archaea)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsRamelot, T.A. / Ding, K. / Magliqui, M. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Lui, J. / Everett, J.K. / Swapna, G. / Acton, T.B. ...Ramelot, T.A. / Ding, K. / Magliqui, M. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Lui, J. / 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: NMR structure of the OB domain of mm0293 from the archea methanosarcina mazei
Authors: Kennedy, M.A. / Ramelot, T.A. / Ding, K. / Magliqui, M. / Jiang, M. / Ciccosanti, C. / Xiao, R. / Lui, J. / Everett, J.K. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionDec 3, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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: Conserved protein


Theoretical massNumber of molelcules
Total (without water)12,5191
Polymers12,5191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 25structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Conserved protein


Mass: 12519.097 Da / Num. of mol.: 1 / Fragment: residues 67-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: Goe1 / Gene: MM0293, MM_0293 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Q045

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D (H)CCH-TOCSY
1613D H(CCO)NH
1713D C(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11012D 1H-15N HSQC
11112D 1H-13C HSQC
11222D 1H-13C HSQC
11314D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 13C; U-100% 15N] OB domain-1, 20 mM MES-2, 100 mM sodium chloride-3, 10 mM DTT-4, 5 mM calcium chloride-5, .02 % sodium azide-6, 95% H2O/5% D2O95% H2O/5% D2O
21.2 mM [U-5% 13C; U-99% 15N] OB domain-7, 20 mM MES-8, 100 mM sodium chloride-9, 10 mM DTT-10, 5 mM calcium chloride-11, .02 % sodium azide-12, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMOB domain-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
10 mMDTT-41
5 mMcalcium chloride-51
.02 %sodium azide-61
1.2 mMOB domain-7[U-5% 13C; U-99% 15N]2
20 mMMES-82
100 mMsodium chloride-92
10 mMDTT-102
5 mMcalcium chloride-112
.02 %sodium azide-122
Sample conditionsIonic strength: .1 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
Sparky3.113Goddarddata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichdata analysis
PSVS1.3Bhattacharya and Montelionedata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIH2.2.1Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: autostructure and cyana were used to automatically assign NOE crosspeaks. xplor-NIH and CNS were used to do hydrogen bond refinement and refinement in the presence of water.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 20

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