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- PDB-2jzt: Solution NMR structure of Q8ZP25_SALTY from Salmonella typhimuriu... -

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Basic information

Entry
Database: PDB / ID: 2jzt
TitleSolution NMR structure of Q8ZP25_SALTY from Salmonella typhimurium. Northeast Structural Genomics Consortium target StR70
ComponentsPutative thiol-disulfide isomerase and thioredoxin
KeywordsISOMERASE / NESG / StR70 / Structural Genomics / Putative [NiFe] hydrogenase assembly / Chaperone / PSI-2 / 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 LT2 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsParish, D. / Liu, G. / Shen, Y. / Ho, C. / Cunningham, K. / Xiao, R. / Swapna, G.V.T. / Acton, T. / Bansal, S. / Prestegard, J.H. ...Parish, D. / Liu, G. / Shen, Y. / Ho, C. / Cunningham, K. / Xiao, R. / Swapna, G.V.T. / Acton, T. / Bansal, S. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2008
Title: Protein chaperones Q8ZP25_SALTY from Salmonella typhimurium and HYAE_ECOLI from Escherichia coli exhibit thioredoxin-like structures despite lack of canonical thioredoxin active site sequence motif.
Authors: Parish, D. / Benach, J. / Liu, G. / Singarapu, K.K. / Xiao, R. / Acton, T. / Su, M. / Bansal, S. / Prestegard, J.H. / Hunt, J. / Montelione, G.T. / Szyperski, T.
History
DepositionJan 16, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative thiol-disulfide isomerase and thioredoxin


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

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Components

#1: Protein Putative thiol-disulfide isomerase and thioredoxin


Mass: 16146.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria)
Species: Salmonella typhimuriumSalmonella enterica subsp. enterica
Strain: LT2 / SGSC1412 / Gene: STM1790 / 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 CABA(CO)NHN
131GFT(4,3)D HABCAB(CO)NHN
141GFT(4,3)D (H)CCH COSY
151Sim 13C,15N-Resolved NOESY
1612D 1H-15N HSQC
1712D 1H-13C HSQC
1822D 1H-13C HSQC
1932D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM 5% 13C; 100% 15N protein, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-5% 13C; U-100% 15N] protein, 15.5 mg/mL phage, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMprotein[U-100% 13C; U-100% 15N]1
1.0 mMprotein5% 13C; 100% 15N2
1 mMprotein[U-5% 13C; U-100% 15N]3
15.5 mg/mLphage3
Sample conditionsIonic strength: 50 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
DYANA1.5Guntert, Braun and Wuthrichdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
VNMR6.1CVariancollection
XEASY1.3Bartels et al.peak picking
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Constrained simulated annealing torsion angle molecular dynamics refinement using xplor, and rdcs refinement using cns and water bath
NMR constraintsNOE constraints total: 1541 / NOE intraresidue total count: 397 / NOE long range total count: 510 / NOE medium range total count: 206 / NOE sequential total count: 428 / Hydrogen bond constraints total count: 10 / Protein chi angle constraints total count: 446 / Protein other angle constraints total count: 528 / Protein phi angle constraints total count: 41 / Protein psi angle constraints total count: 41
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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