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- PDB-2k0z: Solution NMR structure of protein hp1203 from Helicobacter pylori... -

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Basic information

Entry
Database: PDB / ID: 2k0z
TitleSolution NMR structure of protein hp1203 from Helicobacter pylori 26695. Northeast Structural Genomics Consortium (NESG) target PT1/Ontario Center for Structural Proteomics target hp1203
ComponentsUncharacterized protein hp1203
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / a/b domain / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Rhodanese domain-containing protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsWu, B. / Yee, A. / Lemak, A. / Cort, J. / Semest, A. / Kenney, M.A. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of protein hp1203 from Helicobacter pylori 26695. Northeast Structural Genomics Consortium (NESG) target PT1/Ontario Center for Structural Proteomics target hp1203.
Authors: Wu, B. / Yee, A. / Lemak, A. / Cort, J. / Semest, A. / Kenney, M.A. / Arrowsmith, C.H.
History
DepositionFeb 18, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein hp1203


Theoretical massNumber of molelcules
Total (without water)12,9481
Polymers12,9481
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein hp1203


Mass: 12948.499 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_1223 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / References: UniProt: O25821

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HN(CO)CA
1513D HNCA
1613D C(CO)NH
1713D H(CCO)NH
1813D HBHA(CO)NH
1913D HNHA
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY
11213D 1H-15N NOESY
11313D 1H-13C NOESY
1141aiv 3D 1H-13C NOESY
21522D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-99% 13C; U-99% 15N] unknown function protein hp1203 from Helicobacter pylori 26695, 10 mM [U-100% 2H] Tris-HCl, 300 mM sodium chloride, 0.01 % sodium azide, 10 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-7% 13C; U-99% 15N] unknown function protein hp1203 from Helicobacter pylori 26695, 10 mM [U-100% 2H] Tris-HCl, 300 mM sodium chloride, 0.01 % sodium azide, 10 mM benzamidine, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMunknown function protein hp1203 from Helicobacter pylori 26695[U-99% 13C; U-99% 15N]1
10 mMTris-HCl[U-100% 2H]1
300 mMsodium chloride1
0.01 %sodium azide1
10 mMbenzamidine1
0.5 mMunknown function protein hp1203 from Helicobacter pylori 26695[U-7% 13C; U-99% 15N]2
10 mMTris-HCl[U-100% 2H]2
300 mMsodium chloride2
0.01 %sodium azide2
10 mMbenzamidine2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300 7 ambient 298 K
2300 7 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SPARKY3.95Goddarddata analysis
SPARKY3.95Goddardpeak picking
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructure2.1.0Huang, Tejero, Powers and Montelionevalidation
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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