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- PDB-4tr1: Crystal structure of GSH-bound cGrx2/C15S -

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Basic information

Entry
Database: PDB / ID: 4tr1
TitleCrystal structure of GSH-bound cGrx2/C15S
Components(Glutaredoxin 3) x 2
KeywordsOXIDOREDUCTASE / glutaredoxin / GSH
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
GLUTATHIONE / Glutaredoxin
Similarity search - Component
Biological speciesAlkaliphilus oremlandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.582 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 1.2Jan 7, 2015Group: Database references
Revision 1.3Feb 4, 2015Group: Derived calculations
Revision 1.4Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
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_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.classification
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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)21,6914
Polymers21,0762
Non-polymers6152
Water3,531196
1
A: Glutaredoxin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8132
Polymers10,5061
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutaredoxin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8772
Polymers10,5701
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.065, 29.371, 64.836
Angle α, β, γ (deg.)90.000, 118.170, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-220-

HOH

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Components

#1: Protein Glutaredoxin 3 /


Mass: 10505.928 Da / Num. of mol.: 1 / Mutation: C15S
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: Protein Glutaredoxin 3 /


Mass: 10569.990 Da / Num. of mol.: 1 / Mutation: C15S
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
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 0.1 M sodium acetate, pH 5.2, 33% PEG 4000 (w/v), and 0.2 M ammonium acetate.

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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: 1.58→50 Å / Num. obs: 27954 / % possible obs: 97.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.13 Å2 / Net I/σ(I): 39.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementResolution: 1.582→32.356 Å / FOM work R set: 0.8735 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 19.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 1985 7.1 %Random selection
Rwork0.177 25962 --
obs0.179 27947 98.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.23 Å2 / Biso mean: 20.2 Å2 / Biso min: 5.66 Å2
Refinement stepCycle: final / Resolution: 1.582→32.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 40 196 1713
Biso mean--13.85 31.02 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091549
X-RAY DIFFRACTIONf_angle_d1.4492084
X-RAY DIFFRACTIONf_chiral_restr0.087227
X-RAY DIFFRACTIONf_plane_restr0.004264
X-RAY DIFFRACTIONf_dihedral_angle_d16.877573
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5819-1.62150.24071280.20241777190595
1.6215-1.66530.23881390.1961789192897
1.6653-1.71430.22211450.19651826197197
1.7143-1.76960.25281260.20681809193598
1.7696-1.83290.21671500.19261835198598
1.8329-1.90630.24151430.18821837198098
1.9063-1.9930.1971430.18191842198599
1.993-2.09810.24661450.18021894203999
2.0981-2.22950.19991430.17731858200199
2.2295-2.40160.2021430.17781850199399
2.4016-2.64310.22431410.18551890203199
2.6431-3.02540.22961430.18631884202799
3.0254-3.81070.17021500.160518962046100
3.8107-32.36260.17431460.16071975212199

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