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- PDB-2kfp: Solution NMR structure of PSPTO_3016 from Pseudomonas syringae. N... -

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Basic information

Entry
Database: PDB / ID: 2kfp
TitleSolution NMR structure of PSPTO_3016 from Pseudomonas syringae. Northeast Structural Genomics Consortium target PsR293.
ComponentsPSPTO_3016 protein
KeywordsStructural Genomics / UNKNOWN FUNCTION / alpha / beta / double-wing / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyAspartate Aminotransferase, domain 1 - #30 / Uncharacterised protein YjbR / YjbR-like superfamily / YjbR / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta / MmcQ/YjbR family DNA-binding protein
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
MethodSOLUTION NMR / simulated annealing, simulated annealing
Model detailsclosest to the average, model 1
AuthorsFeldmann, E.A. / Ramelot, T.A. / Zhao, L. / Hamilton, K. / Ciccosanti, C. / Xiao, R. / Nair, R. / Everett, J.K. / Swapna, G. / Acton, T.B. ...Feldmann, E.A. / Ramelot, T.A. / Zhao, L. / Hamilton, K. / 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: J.Struct.Funct.Genom. / Year: 2012
Title: Solution NMR and X-ray crystal structures of Pseudomonas syringae Pspto_3016 from protein domain family PF04237 (DUF419) adopt a "double wing" DNA binding motif.
Authors: Feldmann, E.A. / Seetharaman, J. / Ramelot, T.A. / Lew, S. / Zhao, L. / Hamilton, K. / Ciccosanti, C. / Xiao, R. / Acton, T.B. / Everett, J.K. / Tong, L. / Montelione, G.T. / Kennedy, M.A.
History
DepositionFeb 24, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Feb 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 1.4Jun 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 1.5May 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:
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Assembly

Deposited unit
A: PSPTO_3016 protein


Theoretical massNumber of molelcules
Total (without water)14,8301
Polymers14,8301
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 / 150structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein PSPTO_3016 protein


Mass: 14829.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: PSPTO3016, PSPTO_3016 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMGK / References: UniProt: Q880Y4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1322D 1H-13C HSQC
1412D 1H-15N HSQC
1513D 1H-15N NOESY
1613D 1H-13C NOESY
1712D 1H-13C HSQC
1834D CC NOESY
1913D HNCO
11013D HNCA
11113D HN(CA)CB
11213D CBCA(CO)NH
11313D HBHA(CO)NH
11413D (H)CCH-TOCSY
11513D (H)CCH-TOCSY
11613D CBCA(CO)NH
11713D H(CCO)NH
11813D HN(CO)CA
11913D C(CO)NH
12013D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21.1 mM [U-5% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] protein, 20 mM ammonium acetate, 100 mM sodium chloride, 10 mM DTT, 5 mM calcium chloride, 0.02 % sodium azide, 50 uM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMprotein[U-100% 13C; U-100% 15N]1
20 mMammonium acetate1
100 mMsodium chloride1
10 mMDTT1
5 mMcalcium chloride1
0.02 %sodium azide1
50 uMDSS1
1.1 mMprotein[U-5% 13C; U-100% 15N]2
20 mMammonium acetate2
100 mMsodium chloride2
10 mMDTT2
5 mMcalcium chloride2
0.02 %sodium azide2
50 uMDSS2
1.0 mMprotein[U-100% 13C; U-100% 15N]3
20 mMammonium acetate3
100 mMsodium chloride3
10 mMDTT3
5 mMcalcium chloride3
0.02 %sodium azide3
50 uMDSS3
Sample conditionsIonic strength: .1 / 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
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.3Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure solution
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PSVS1.3Bhattacharya and Montelionerefinement
RefinementMethod: simulated annealing, simulated annealing / Software ordinal: 1 / Details: Xplor-NIH, Xplor-NIH HBDA Torsion Angle Refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20

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