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- PDB-2klx: Solution structure of glutaredoxin from Bartonella henselae str. ... -

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Basic information

Entry
Database: PDB / ID: 2klx
TitleSolution structure of glutaredoxin from Bartonella henselae str. Houston
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / glutaredoxin / thioredoxin type domain / SSGCID / electron transport / structural genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glutathione disulfide oxidoreductase activity / protein-disulfide reductase activity / cell redox homeostasis / cellular response to oxidative stress / electron transfer activity / cytoplasm
Similarity search - Function
Glutaredoxin, GrxC / Glutaredoxin subgroup / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Glutaredoxin, GrxC / Glutaredoxin subgroup / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutaredoxin / Glutaredoxin
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLeeper, T.C. / Varani, G. / Zheng, S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Comparative analysis of glutaredoxin domains from bacterial opportunistic pathogens.
Authors: Leeper, T. / Zhang, S. / Van Voorhis, W.C. / Myler, P.J. / Varani, G.
History
DepositionJul 10, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaredoxin


Theoretical massNumber of molelcules
Total (without water)10,0781
Polymers10,0781
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Glutaredoxin


Mass: 10078.468 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: Houston-1 / Description: protein cleaved with 3C protease / Gene: grxC, BH04010 / Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: UniProt: Q6G5J5, UniProt: A0A0H3LXP0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N TOCSY
1213D 1H-15N NOESY
1312D 1H-15N HSQC
1412D 1H-13C HSQC
1513D HNCO
1613D HNCA
1713D HN(CO)CA
1813D CBCA(CO)NH
1913D HN(CA)CB
11013D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] protein, 100 mM potassium phosphate, 10 mM potassium chloride, 8 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-98% 13C; U-98% 15N] protein, 100 mM potassium phosphate, 10 mM potassium chloride, 8 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-100% 15N]1
100 mMpotassium phosphate-21
10 mMpotassium chloride-31
8 %D2O-41
0.8 mMentity-5[U-98% 13C; U-98% 15N]2
100 mMpotassium phosphate-62
10 mMpotassium chloride-72
8 %D2O-82
Sample conditionsIonic strength: 110 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE7503

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
SparkyCCPNchemical shift assignment
TopSpinBruker Biospincollection
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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