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- PDB-5kqa: Crystal structure of buckwheat glutaredoxin-glutathione complex -

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Basic information

Entry
Database: PDB / ID: 5kqa
TitleCrystal structure of buckwheat glutaredoxin-glutathione complex
ComponentsGlutaredoxin-glutathione complex
KeywordsOXIDOREDUCTASE / Glutaredoxin / glutathione / complex / monomer
Function / homology
Function and homology information


glutathione disulfide oxidoreductase activity / cellular response to oxidative stress / 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
GLUTATHIONE / Glutaredoxin
Similarity search - Component
Biological speciesPolygonaceae (buckwheat family)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZhang, X. / Wang, W. / Zhao, Y. / Wang, Z. / Wang, H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China2014DFA30270 China
National Natural Science Foundation of China21543003 China
Hundred Talent Plans and Research Projects of Shanxi Province2015081049 China
CitationJournal: J. Inorg. Biochem. / Year: 2017
Title: Structural insights into the binding of buckwheat glutaredoxin with GSH and regulation of its catalytic activity
Authors: Zhang, X. / Wang, W. / Li, C. / Zhao, Y. / Yuan, H. / Tan, X. / Wu, L. / Wang, Z. / Wang, H.
History
DepositionJul 6, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 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
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-glutathione complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4542
Polymers14,1471
Non-polymers3071
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-4 kcal/mol
Surface area6160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.011, 92.299, 28.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glutaredoxin-glutathione complex


Mass: 14147.089 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polygonaceae (buckwheat family) / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1W6I4R7*PLUS
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KX517761 FOR THIS SEQUENCE. THE CONSTRUCT WAS EXPRESSED WITH THE EXPRESSION GST TAG.

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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: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.1M CH3COONa pH=4.5 20%-24% PEG3350 (W/V)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 7521 / % possible obs: 98.53 % / Redundancy: 5.4 % / Net I/σ(I): 32
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 17.39 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2e7p

2e7p


Resolution: 2.05→38.986 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 18.89
RfactorNum. reflection% reflection
Rfree0.2162 738 10 %
Rwork0.1628 --
obs0.1682 7380 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→38.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms847 0 20 95 962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007879
X-RAY DIFFRACTIONf_angle_d0.991182
X-RAY DIFFRACTIONf_dihedral_angle_d13.693328
X-RAY DIFFRACTIONf_chiral_restr0.033132
X-RAY DIFFRACTIONf_plane_restr0.004154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0503-2.20850.24331420.15591281X-RAY DIFFRACTION98
2.2085-2.43080.21811460.1511315X-RAY DIFFRACTION100
2.4308-2.78240.25091470.17191318X-RAY DIFFRACTION100
2.7824-3.50520.21311490.17261342X-RAY DIFFRACTION99
3.5052-38.99290.1911540.15881386X-RAY DIFFRACTION97

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