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- PDB-2gzp: Solution NMR structure of Q8ZP25 from Salmonella typhimurium LT2;... -

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Basic information

Entry
Database: PDB / ID: 2gzp
TitleSolution NMR structure of Q8ZP25 from Salmonella typhimurium LT2; Northeast Structural Genomics Consortium Target STR70
Componentsputative chaperone
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / GFT-NMR / Putative thiol-disulfide isomerase / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology[NiFe]-hydrogenase maturation factor HyaE / Hydrogenase-1 expression protein HyaE / isomerase activity / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Thiol-disulfide isomerase and thioredoxin
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / constrained simulated annealing torsion angle dynamics molecular dynamics water bath refinement
AuthorsParish, D. / Liu, G. / Shen, Y. / Ho, C. / Cunningham, K. / Xiao, R. / Swapna, G.V.T. / Acton, T.B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of Q8ZP24 from Salmonella typhimurium LT2.
Authors: Parish, D. / Liu, G. / Shen, Y. / Ho, C.K. / Cunningham, K. / Xiao, R. / Swapna, G.V.T. / Acton, T.B. / Montelione, G.T. / Szyperski, T.
History
DepositionMay 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: putative chaperone


Theoretical massNumber of molelcules
Total (without water)16,1461
Polymers16,1461
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein putative chaperone


Mass: 16146.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: Q8ZP25 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 +magic / References: UniProt: Q8ZP25

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111GFT (4,3)D HNNCABCA
121GFT (4,3)D CABCA(CO)NHN
131GFT (4,3)D HABCAB(CO)NHN
141GFT (4,3)D (H)CCH
151SIM 13C-, 15N-resolved [1H, 1H] NOESY
161Aromatic 13C-Resolved [1H, 1H] NOESY

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Sample preparation

DetailsContents: NMR Buffer, PH 6.5, 95% H20, 5% D20 / Solvent system: 95% H20, 5% D20
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 27 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, DeLano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warren.refinement
DYANA1.5Guntertstructure solution
CYANA1.05Guntertstructure solution
CYANA2.1Guntertstructure solution
VNMR6.1cVariancollection
NMRPipe2.3Delaglio, Baxprocessing
XEASY1.3.1.3Glaserdata analysis
AutoStructure2.0.0Huang, Tejero, Power, Montelionedata analysis
AutoAssignZimmerman, Moseley, Kiriyeva, Kulikowski, Montelionedata analysis
RefinementMethod: constrained simulated annealing torsion angle dynamics molecular dynamics water bath refinement
Software ordinal: 1
Details: distance constraints from NOEs angle constraints for clear secondary structure only stereospecific assignments based on glomsa (HB) and partially labeled sample (QG,QD)
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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