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- PDB-7yp0: Crystal structure of CtGST -

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Basic information

Entry
Database: PDB / ID: 7yp0
TitleCrystal structure of CtGST
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / Deoxynivaneol detoxification enzyme / glutathione S-transferase
Function / homology: / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / transferase activity / Thioredoxin-like superfamily / Glutathione S-transferase
Function and homology information
Biological speciesColletotrichum tofieldiae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYang, J. / Fan, J.P. / Lei, X.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Jacs Au / Year: 2024
Title: Enzymatic Degradation of Deoxynivalenol with the Engineered Detoxification Enzyme Fhb7.
Authors: Yang, J. / Liang, K. / Ke, H. / Zhang, Y. / Meng, Q. / Gao, L. / Fan, J. / Li, G. / Zhou, H. / Xiao, J. / Lei, X.
History
DepositionAug 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase
B: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)62,7752
Polymers62,7752
Non-polymers00
Water3,405189
1
A: Glutathione S-transferase

B: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)62,7752
Polymers62,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y,-z+1/21
Buried area1320 Å2
ΔGint-10 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.428, 133.870, 143.099
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2

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Components

#1: Protein Glutathione S-transferase / GST


Mass: 31387.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colletotrichum tofieldiae (fungus) / Gene: CT0861_04895 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A166URZ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 3.11 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate (pH 4.6), 1.2 M ammonium phosphate monobasic, 0.3 M sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 34935 / % possible obs: 1 % / Redundancy: 12.1 % / Biso Wilson estimate: 29.51 Å2 / CC1/2: 0.999 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 1707 / CC1/2: 0.782

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YOC

7yoc


Resolution: 2.3→26.87 Å / SU ML: 0.2272 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.5373
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2191 1988 5.78 %
Rwork0.1862 32432 -
obs0.1881 34420 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 0 189 4213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094144
X-RAY DIFFRACTIONf_angle_d1.08415661
X-RAY DIFFRACTIONf_chiral_restr0.0584624
X-RAY DIFFRACTIONf_plane_restr0.0119731
X-RAY DIFFRACTIONf_dihedral_angle_d6.9713549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.27681110.21011768X-RAY DIFFRACTION74.56
2.35-2.420.26621170.20952191X-RAY DIFFRACTION93.33
2.42-2.490.22891560.19622280X-RAY DIFFRACTION97.95
2.49-2.570.2481460.2092327X-RAY DIFFRACTION99.44
2.57-2.660.2381340.21522361X-RAY DIFFRACTION99.92
2.66-2.770.24251460.21172330X-RAY DIFFRACTION99.96
2.77-2.890.23471390.2082388X-RAY DIFFRACTION99.92
2.89-3.040.26991530.2032352X-RAY DIFFRACTION100
3.04-3.230.23171430.20222356X-RAY DIFFRACTION99.96
3.23-3.480.22951390.1922378X-RAY DIFFRACTION100
3.48-3.830.19751530.1792374X-RAY DIFFRACTION100
3.83-4.390.20661470.15792397X-RAY DIFFRACTION100
4.39-5.520.19811500.16352410X-RAY DIFFRACTION99.96
5.52-26.870.18031540.17592520X-RAY DIFFRACTION99.63

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