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- PDB-1qfn: GLUTAREDOXIN-1-RIBONUCLEOTIDE REDUCTASE B1 MIXED DISULFIDE BOND -

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Basic information

Entry
Database: PDB / ID: 1qfn
TitleGLUTAREDOXIN-1-RIBONUCLEOTIDE REDUCTASE B1 MIXED DISULFIDE BOND
Components
  • PROTEIN (GLUTAREDOXIN 1)
  • PROTEIN (RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1)
KeywordsELECTRON TRANSPORT/OXIDOREDUCTASE / GLUTAREDOXIN / RIBONUCLEOTIDE REDUCTASE / DISULFIDE / ELECTRON TRANSFER / ELECTRON TRANSPORT-OXIDOREDUCTASE COMPLEX
Function / homology
Function and homology information


cysteine biosynthetic process via S-sulfo-L-cysteine / sulfate assimilation via adenylyl sulfate reduction / protein-disulfide reductase (glutathione) activity / glutathione disulfide oxidoreductase activity / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / disulfide oxidoreductase activity / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase ...cysteine biosynthetic process via S-sulfo-L-cysteine / sulfate assimilation via adenylyl sulfate reduction / protein-disulfide reductase (glutathione) activity / glutathione disulfide oxidoreductase activity / ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / disulfide oxidoreductase activity / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein-disulfide reductase activity / protein folding chaperone / cell redox homeostasis / cellular response to oxidative stress / electron transfer activity / nucleotide binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Glutaredoxin, GrxA / Glutaredoxin subgroup / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Glutaredoxin active site / Glutaredoxin active site. / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit ...Glutaredoxin, GrxA / Glutaredoxin subgroup / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Glutaredoxin active site / Glutaredoxin active site. / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Glutaredoxin / Glutaredoxin / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase 1 subunit alpha / Glutaredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / RESTRICTED TORSIONAL ANGLE DYNAMICS
AuthorsBerardi, M.J. / Bushweller, J.H.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Binding specificity and mechanistic insight into glutaredoxin-catalyzed protein disulfide reduction.
Authors: Berardi, M.J. / Bushweller, J.H.
History
DepositionApr 12, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GLUTAREDOXIN 1)
B: PROTEIN (RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1)


Theoretical massNumber of molelcules
Total (without water)12,2012
Polymers12,2012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50LEAST TARGET FUNCTION
RepresentativeModel #1

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Components

#1: Protein PROTEIN (GLUTAREDOXIN 1) / GRX 1


Mass: 9679.759 Da / Num. of mol.: 1 / Mutation: C14S
Source method: isolated from a genetically manipulated source
Details: INTERMOLECULAR DISULFIDE BRIDGE BETWEEN; CYS 11 A AND CYS 148 B
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P68688
#2: Protein/peptide PROTEIN (RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1) / E.C.1.17.4.1 / Ribonucleotide reductase / B1 protein / R1 protein


Mass: 2521.603 Da / Num. of mol.: 1 / Fragment: apha chain, B1 SUBUNIT / Mutation: C754S
Source method: isolated from a genetically manipulated source
Details: INTERMOLECULAR DISULFIDE BRIDGE CYS759 / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P00452, ribonucleoside-diphosphate reductase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR software
NameVersionDeveloperClassification
OPALV2.6P.LUGINBUHL,P.GUNTERT,M.BILLETER,K.WUTHRICHrefinement
DYANAstructure solution
RefinementMethod: RESTRICTED TORSIONAL ANGLE DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST TARGET FUNCTION / Conformers calculated total number: 50 / Conformers submitted total number: 20

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