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- PDB-3grx: NMR STRUCTURE OF ESCHERICHIA COLI GLUTAREDOXIN 3-GLUTATHIONE MIXE... -

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Basic information

Entry
Database: PDB / ID: 3grx
TitleNMR STRUCTURE OF ESCHERICHIA COLI GLUTAREDOXIN 3-GLUTATHIONE MIXED DISULFIDE COMPLEX, 20 STRUCTURES
ComponentsGLUTAREDOXIN 3
KeywordsELECTRON TRANSPORT / THIOL-DISULFIDE OXIDOREDUCTASE / THIOLTRANSFERASE / THIOREDOXIN SUPERFAMILY
Function / homology
Function and homology information


glutathione disulfide oxidoreductase activity / glutathione binding / deoxyribonucleotide biosynthetic process / protein-disulfide reductase activity / cell redox homeostasis / cellular response to oxidative stress / cytoplasm / cytosol
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
GLUTATHIONE / Glutaredoxin 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNordstrand, K. / Aslund, F. / Holmgren, A. / Otting, G. / Berndt, K.D.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: NMR structure of Escherichia coli glutaredoxin 3-glutathione mixed disulfide complex: implications for the enzymatic mechanism.
Authors: Nordstrand, K. / slund, F. / Holmgren, A. / Otting, G. / Berndt, K.D.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Glutaredoxin-3 from Escherichia Coli. Amino Acid Sequence, 1H and 15N NMR Assignments, and Structural Analysis
Authors: Aslund, F. / Nordstrand, K. / Berndt, K.D. / Nikkola, M. / Bergman, T. / Ponstingl, H. / Jornvall, H. / Otting, G. / Holmgren, A.
History
DepositionAug 17, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 18, 2012Group: Non-polymer description
Revision 1.4Mar 14, 2018Group: Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.5Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAREDOXIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3712
Polymers9,0631
Non-polymers3071
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 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein GLUTAREDOXIN 3


Mass: 9063.272 Da / Num. of mol.: 1 / Mutation: C14S, C65Y
Source method: isolated from a genetically manipulated source
Details: COVALENT COMPLEX WITH GLUTATHIONE / Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: BL21 / Plasmid: PET-24D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0AC62
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1213QF-COSY
131SMALL FLIP ANGLE COSY
141TOCSY
151NOESY
161OMEGA1-DECOUPLED NOESY
1712D HNHB
18115N-HSQC
191NOESY-15N-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING ONE SAMPLE OF RECOMBINANT GRX3[C14S/C65Y] AT NATURAL ABUNDANCE AND ONE SAMPLE OF UNIFORMLY 15N-LABELED GRX3[C14S/C65Y] COMPLEXED WITH UNLABELED GLUTATHIONE.

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Sample preparation

DetailsContents: H2O/D2O
Sample conditionsIonic strength: 0.05 M / pH: 6 / Pressure: 1 atm / Temperature: 301 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX 600 / Manufacturer: Bruker / Model: DMX 600 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
OPALLUGINBUHL,GUNTERT,BILLETER, WUTHRICHrefinement
XEASYstructure solution
DYANAstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THE 20 CONFORMERS WERE ENERGY-MINIMIZED IN A 6 ANGSTROM SHELL OF EXPLICIT WATER.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 20

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