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- PDB-5zvl: Crystal Structure of Wheat Glutarredoxin -

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Basic information

Entry
Database: PDB / ID: 5zvl
TitleCrystal Structure of Wheat Glutarredoxin
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / glutarredoxin / thioreducins
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 active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / 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
Glutaredoxin domain-containing protein / Glutaredoxin
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.963 Å
AuthorsHu, S.Q. / Sun, X.M. / Chen, M.R.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31471691 China
National Natural Science Foundation of China31771906 China
CitationJournal: J. Agric. Food Chem. / Year: 2018
Title: Crystal Structure of Wheat Glutaredoxin and Its Application in Improving the Processing Quality of Flour.
Authors: Sun, X. / Chen, M. / Jia, F. / Hou, Y. / Hu, S.Q.
History
DepositionMay 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Oct 23, 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: Glutaredoxin
B: Glutaredoxin
C: Glutaredoxin
D: Glutaredoxin
E: Glutaredoxin


Theoretical massNumber of molelcules
Total (without water)91,7145
Polymers91,7145
Non-polymers00
Water1,42379
1
A: Glutaredoxin


Theoretical massNumber of molelcules
Total (without water)18,3431
Polymers18,3431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaredoxin


Theoretical massNumber of molelcules
Total (without water)18,3431
Polymers18,3431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutaredoxin


Theoretical massNumber of molelcules
Total (without water)18,3431
Polymers18,3431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glutaredoxin


Theoretical massNumber of molelcules
Total (without water)18,3431
Polymers18,3431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glutaredoxin


Theoretical massNumber of molelcules
Total (without water)18,3431
Polymers18,3431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.557, 173.636, 175.708
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-205-

HOH

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Components

#1: Protein
Glutaredoxin


Mass: 18342.715 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: The gene was cloned from wheat seedling, the coded protein is a homolog.
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: B5A8A6, UniProt: A0A3B6C9E7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.85 Å3/Da / Density % sol: 68.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.65 M ammonium sulfate, 0.08 M Sodium acetate, pH 4.6, 20% glycerol, and 10 mM GSH

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 29640 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.94 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.027 / Rrim(I) all: 0.098 / Χ2: 0.956 / Net I/σ(I): 27.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.94-2.9912.40.6953.7114470.9390.2040.7250.848100
2.99-3.0512.40.6614800.9390.1940.6880.84599.9
3.05-3.111.90.53114520.9540.1590.5550.88899.9
3.1-3.1712.60.48414550.970.1410.5050.904100
3.17-3.2413.90.45814590.9770.1270.4750.875100
3.24-3.3113.80.35414550.9840.0990.3680.932100
3.31-3.3913.80.28714690.9880.0810.2980.943100
3.39-3.4913.70.22714670.9910.0640.2361.012100
3.49-3.5913.60.18514690.9930.0520.1931.039100
3.59-3.713.40.1714700.9940.0490.1771.315100
3.7-3.8413.30.12714930.9960.0370.1321.074100
3.84-3.9912.70.11714690.9960.0340.1221.156100
3.99-4.1712.20.10614730.9910.0320.1111.10299.9
4.17-4.3913.90.0914880.9980.0250.0941.04100
4.39-4.6713.80.07914740.9970.0220.0821.037100
4.67-5.0313.60.07714890.9970.0220.081.013100
5.03-5.5313.20.07114930.9970.020.0740.892100
5.53-6.3311.90.06615070.9980.020.0690.83100
6.33-7.9713.60.05715250.9980.0160.0590.71799.9
7.97-5011.50.04616060.9990.0140.0480.61999.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E7P

2e7p


Resolution: 2.963→31.86 Å / FOM work R set: 0.7696 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2789 1810 6.86 %
Rwork0.2538 24571 -
obs0.2554 26381 88.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.01 Å2 / Biso mean: 45.59 Å2 / Biso min: 11.96 Å2
Refinement stepCycle: final / Resolution: 2.963→31.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 0 79 3961
Biso mean---40.71 -
Num. residues----527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0253943
X-RAY DIFFRACTIONf_angle_d2.1365336
X-RAY DIFFRACTIONf_chiral_restr0.127642
X-RAY DIFFRACTIONf_plane_restr0.01677
X-RAY DIFFRACTIONf_dihedral_angle_d19.8311409
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9626-3.04260.41191010.34261191129257
3.0426-3.13210.3438950.33211392148766
3.1321-3.23310.34281180.3431482160071
3.2331-3.34850.42941220.30741663178579
3.3485-3.48240.30421320.29151821195386
3.4824-3.64070.29361330.27062012214594
3.6407-3.83240.261610.25882068222999
3.8324-4.0720.24911580.242421172275100
4.072-4.38570.27041660.243721502316100
4.3857-4.82570.22511250.212321622287100
4.8257-5.52080.26031950.236921242319100
5.5208-6.94380.29491360.270521942330100
6.9438-31.86180.25111680.21372195236397

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