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- PDB-8k2p: Crystal structure of CtGST-F76A -

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Basic information

Entry
Database: PDB / ID: 8k2p
TitleCrystal structure of CtGST-F76A
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / Deoxynivaneol detoxification enzyme / glutathione S-transferase / Fusarium head blight resistance
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: 2.2 Å
AuthorsYang, J. / Xiao, J.Y. / Lei, X.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22193073 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
DepositionJul 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,6232
Polymers62,6232
Non-polymers00
Water3,171176
1
A: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)31,3111
Polymers31,3111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)31,3111
Polymers31,3111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.481, 133.562, 143.386
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-413-

HOH

21B-416-

HOH

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Components

#1: Protein Glutathione S-transferase


Mass: 31311.475 Da / Num. of mol.: 2 / Mutation: F76A
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.: 176 / 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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5 M Lithium sulfate, 0.1 M Trisodium citrate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→66.78 Å / Num. obs: 37444 / % possible obs: 94 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.027 / Rrim(I) all: 0.097 / Χ2: 0.94 / Net I/σ(I): 18.7 / Num. measured all: 490916
Reflection shellResolution: 2.2→2.31 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.098 / Num. unique obs: 4096 / CC1/2: 0.868 / Rpim(I) all: 0.32 / Rrim(I) all: 0.097 / Χ2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.58 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 2005 5.36 %
Rwork0.2029 --
obs0.2052 37404 93.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→32.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3965 0 0 176 4141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d6.099542
X-RAY DIFFRACTIONf_chiral_restr0.053617
X-RAY DIFFRACTIONf_plane_restr0.011720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.40391160.3241783X-RAY DIFFRACTION100
2.27-2.310.2735920.271969X-RAY DIFFRACTION100
2.31-2.380.2681580.23932649X-RAY DIFFRACTION100
2.38-2.460.27051430.22722682X-RAY DIFFRACTION100
2.46-2.540.2921520.23662644X-RAY DIFFRACTION100
2.54-2.650.30151610.23052658X-RAY DIFFRACTION100
2.65-2.770.2561470.23282671X-RAY DIFFRACTION100
2.77-2.910.29751520.21532677X-RAY DIFFRACTION100
2.91-3.090.2661450.20462692X-RAY DIFFRACTION100
3.09-3.330.27161600.2122677X-RAY DIFFRACTION100
3.33-3.650.24841440.18232577X-RAY DIFFRACTION99
3.69-4.20.21931260.17622135X-RAY DIFFRACTION82
4.2-5.280.20531530.17462744X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -9.5024 Å / Origin y: 0.3062 Å / Origin z: 16.1329 Å
111213212223313233
T0.3069 Å20.0095 Å2-0.0235 Å2-0.2899 Å20.005 Å2--0.2734 Å2
L0.1331 °20.0525 °20.0138 °2-0.5882 °2-0.2844 °2--0.132 °2
S0.0419 Å °0.0153 Å °-0.0198 Å °-0.0838 Å °-0.0007 Å °-0.0269 Å °0.0696 Å °-0.0326 Å °0 Å °
Refinement TLS groupSelection details: all

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