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- PDB-2kpu: NMR Structure of YbbR family protein Dhaf_0833 (residues 32-118) ... -

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Basic information

Entry
Database: PDB / ID: 2kpu
TitleNMR Structure of YbbR family protein Dhaf_0833 (residues 32-118) from Desulfitobacterium hafniense DCB-2: Northeast Structural Genomics Consortium target DhR29B
ComponentsYbbR family protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyRNA Polymerase Alpha Subunit; Chain A, domain 2 - #30 / YbbR-like / YbbR-like protein / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Beta Complex / Mainly Beta / YbbR family protein
Function and homology information
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsno criteria, model 1
AuthorsCort, J.R. / Ramelot, T.A. / Yang, Y. / Belote, R.L. / Ciccosanti, C. / Haleema, J. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Cort, J.R. / Ramelot, T.A. / Yang, Y. / Belote, R.L. / Ciccosanti, C. / Haleema, J. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Protein Sci. / Year: 2011
Title: Structures of domains I and IV from YbbR are representative of a widely distributed protein family.
Authors: Barb, A.W. / Cort, J.R. / Seetharaman, J. / Lew, S. / Lee, H.W. / Acton, T. / Xiao, R. / Kennedy, M.A. / Tong, L. / Montelione, G.T. / Prestegard, J.H.
History
DepositionOct 20, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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: YbbR family protein


Theoretical massNumber of molelcules
Total (without water)10,7911
Polymers10,7911
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 / 40low energy, few restraint violations, favorable geometry
RepresentativeModel #1no criteria

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Components

#1: Protein YbbR family protein


Mass: 10791.182 Da / Num. of mol.: 1 / Fragment: sequence database residues 32-118
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB-2 / Gene: Dhaf_0833, Dhaf_0833 (32-118) / Production host: Escherichia coli (E. coli) / References: UniProt: B8FX10

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: structure of fragment 32-118 of the full length protein (437 residues)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11124D 1H-13C-13C-1H HMQC-NOESY-HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] Dhaf_0833 (32-118), 20 mM ammonium acetate, 200 mM sodium chloride-3, 10 mM calcium chloride-4, 0.02 % sodium azide-5, 95% H2O/5% D2O95% H2O/5% D2O
20.8 mM [U-100% 13C; U-100% 15N] Dhaf_0833 (32-118), 20 mM ammonium acetate, 200 mM sodium chloride, 10 mM calcium chloride, 0.02 % sodium azide, 100% D2O100% D2O
30.8 mM [5% 13C from 5% U-13C glucose in growth medium; U-100% 15N] Dhaf_0833 (32-118), 20 mM ammonium acetate, 200 mM sodium chloride, 10 mM calcium chloride, 0.02 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMDhaf_0833 (32-118)-1[U-100% 13C; U-100% 15N]1
20 mMammonium acetate-21
200 mMsodium chloride-31
10 mMcalcium chloride-41
0.02 %sodium azide-51
0.8 mMDhaf_0833 (32-118)-6[U-100% 13C; U-100% 15N]2
20 mMammonium acetate-72
200 mMsodium chloride-82
10 mMcalcium chloride-92
0.02 %sodium azide-102
0.8 mMDhaf_0833 (32-118)-11[5% 13C from 5% U-13C glucose in growth medium; U-100% 15N]3
20 mMammonium acetate-123
200 mMsodium chloride-133
10 mMcalcium chloride-143
0.02 %sodium azide-153
Sample conditionsIonic strength: 0.23 / pH: 4.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Bruker AvanceBrukerAVANCE8503

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Processing

NMR software
NameDeveloperClassification
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVSBhattacharya and Montelionerefinement
FelixAccelrys Software Inc.processing
SparkyGoddarddata analysis
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: no criteria
NMR ensembleConformer selection criteria: low energy, few restraint violations, favorable geometry
Conformers calculated total number: 40 / Conformers submitted total number: 20

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