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- PDB-1z7r: Solution Structure of reduced glutaredoxin C1 from Populus tremul... -

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Basic information

Entry
Database: PDB / ID: 1z7r
TitleSolution Structure of reduced glutaredoxin C1 from Populus tremula x tremuloides
Componentsglutaredoxin
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


glutathione disulfide oxidoreductase activity / 2 iron, 2 sulfur cluster binding / cellular response to oxidative stress / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPopulus tremula x Populus tremuloides (plant)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model type detailsminimized average
AuthorsFeng, Y. / Zhong, N. / Rouhier, N. / Jacquot, J.P. / Xia, B.
CitationJournal: Biochemistry / Year: 2006
Title: Structural Insight into Poplar Glutaredoxin C1 with a Bridging Iron-Sulfur Cluster at the Active Site
Authors: Feng, Y. / Zhong, N. / Rouhier, N. / Hase, T. / Kusunoki, M. / Jacquot, J.P. / Jin, C. / Xia, B.
History
DepositionMar 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)12,5291
Polymers12,5291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein glutaredoxin / glutaredoxin C1


Mass: 12529.306 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus tremula x Populus tremuloides (plant)
Plasmid: pET3d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5PSJ1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1313D 13C-separated NOESY in aromatic region

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Sample preparation

DetailsContents: 1.1mM uniformly 13C/15N-labeled protein, 40mM potassium phosphate buffer, 90% H2O/10% D2O, 40mM DTT, 0.01% NaN3 and 0.01% DSS, protease inhibitor cocktail
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 40mM potassium phosphate / pH: 6.4 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6Guntert, P.structure solution
Amber7Case, D. A.refinement
NMRView5.2.2Johnson, B. A.data analysis
NMRPipe2.3Delaglio, F.processing
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: CYS 31 is present as the thiolate with a negative charge on the sulfur.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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