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- PDB-5gtx: Crystal structure of mutated buckwheat glutaredoxin -

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Basic information

Entry
Database: PDB / ID: 5gtx
TitleCrystal structure of mutated buckwheat glutaredoxin
Componentsbuckwheat glutaredoxin
KeywordsOXIDOREDUCTASE / Glutaredoxin / glutathione / enzymatic activity
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
Biological speciesPolygonaceae (buckwheat family)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsZhang, X. / Wang, W. / Zhao, Y. / Wang, Z. / Wang, H.
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
DepositionAug 23, 2016Deposition site: PDBJ / 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: buckwheat glutaredoxin
B: buckwheat glutaredoxin


Theoretical massNumber of molelcules
Total (without water)27,7402
Polymers27,7402
Non-polymers00
Water48627
1
A: buckwheat glutaredoxin


Theoretical massNumber of molelcules
Total (without water)13,8701
Polymers13,8701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: buckwheat glutaredoxin


Theoretical massNumber of molelcules
Total (without water)13,8701
Polymers13,8701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.251, 62.185, 143.407
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein buckwheat glutaredoxin


Mass: 13869.790 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polygonaceae (buckwheat family) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1W6I4R7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS KX517761 FOR THIS SEQUENCE.

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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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 300 K / Method: liquid diffusion / Details: 100mM CH3COONa pH4.5 and 23%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 11059 / % possible obs: 100 % / Redundancy: 12.7 % / Net I/σ(I): 29.8
Reflection shellResolution: 2.28→2.34 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 3.67 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.10.1-2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KQA

5kqa


Resolution: 2.28→40.447 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.84
RfactorNum. reflection% reflection
Rfree0.2422 551 5 %
Rwork0.2129 --
obs0.2145 11024 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.28→40.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 0 27 1719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071718
X-RAY DIFFRACTIONf_angle_d0.8972314
X-RAY DIFFRACTIONf_dihedral_angle_d18.5541046
X-RAY DIFFRACTIONf_chiral_restr0.05260
X-RAY DIFFRACTIONf_plane_restr0.006300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.51880.25751290.2572518X-RAY DIFFRACTION97
2.5188-2.88320.33221320.2692590X-RAY DIFFRACTION100
2.8832-3.63220.24881480.22472617X-RAY DIFFRACTION100
3.6322-40.45370.21391420.18592748X-RAY DIFFRACTION100

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