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- PDB-4tr0: Crystal structure of GSSG-bound cGrx2 -

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Basic information

Entry
Database: PDB / ID: 4tr0
TitleCrystal structure of GSSG-bound cGrx2
ComponentsGlutaredoxin 3
KeywordsOXIDOREDUCTASE / Glutaredoxin / GSSG
Function / homology
Function and homology information


glutathione disulfide oxidoreductase activity / cell redox homeostasis / 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
ACETATE ION / OXIDIZED GLUTATHIONE DISULFIDE / Glutaredoxin
Similarity search - Component
Biological speciesAlkaliphilus oremlandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsLee, E.H. / Hwang, K.Y.
CitationJournal: Arch.Biochem.Biophys. / Year: 2014
Title: The GSH- and GSSG-bound structures of glutaredoxin from Clostridium oremlandii.
Authors: Lee, E.H. / Kim, H.Y. / Hwang, K.Y.
History
DepositionJun 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaredoxin 3
B: Glutaredoxin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6646
Polymers21,3202
Non-polymers1,3434
Water3,981221
1
A: Glutaredoxin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3323
Polymers10,6601
Non-polymers6722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutaredoxin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3323
Polymers10,6601
Non-polymers6722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.848, 64.007, 44.462
Angle α, β, γ (deg.)90.000, 103.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

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Components

#1: Protein Glutaredoxin 3 /


Mass: 10660.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkaliphilus oremlandii (bacteria) / Strain: OhILAs / Gene: Clos_2422 / Plasmid: pET21b / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) star / References: UniProt: A8MJH2
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GDS / OXIDIZED GLUTATHIONE DISULFIDE / Glutathione disulfide


Mass: 612.631 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32N6O12S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 28% PEG 400 (w/v), and 0.2 M calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 19791 / % possible obs: 90.6 % / Redundancy: 2 % / Biso Wilson estimate: 20.27 Å2 / Net I/σ(I): 18.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KTE

1kte


Resolution: 1.951→19.642 Å / FOM work R set: 0.8939 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 18.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 1004 5.15 %Random selection
Rwork0.1502 18480 --
obs0.1525 19484 90.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.73 Å2 / Biso mean: 19.56 Å2 / Biso min: 2.48 Å2
Refinement stepCycle: final / Resolution: 1.951→19.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 88 221 1783
Biso mean--35.24 28.85 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191594
X-RAY DIFFRACTIONf_angle_d1.7372136
X-RAY DIFFRACTIONf_chiral_restr0.115230
X-RAY DIFFRACTIONf_plane_restr0.007274
X-RAY DIFFRACTIONf_dihedral_angle_d24.066592
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9512-2.0540.25631340.19222349248381
2.054-2.18250.2341350.15792505264087
2.1825-2.35080.18331410.15072626276790
2.3508-2.58690.20651490.15052632278191
2.5869-2.96010.20551450.16382690283592
2.9601-3.72530.19671520.14252809296196
3.7253-19.64290.16581480.13912869301796

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