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- PDB-7yoc: Crystal structure of Fhb7 -

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Basic information

Entry
Database: PDB / ID: 7yoc
TitleCrystal structure of Fhb7
ComponentsFhb7
KeywordsTRANSFERASE / Deoxynivaneol detoxification enzyme / glutathione S-transferase / Fusarium head blight resistance
Biological speciesThinopyrum elongatum (tall wheatgrass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsYang, J. / Liang, K. / 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
DepositionAug 1, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fhb7
B: Fhb7


Theoretical massNumber of molelcules
Total (without water)61,9972
Polymers61,9972
Non-polymers00
Water1,946108
1
A: Fhb7


Theoretical massNumber of molelcules
Total (without water)30,9981
Polymers30,9981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fhb7


Theoretical massNumber of molelcules
Total (without water)30,9981
Polymers30,9981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.085, 116.908, 139.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 9 through 50 or (resid 51...
d_2ens_1(chain "B" and (resid 9 through 165 or resid 200 through 281))

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Components

#1: Protein Fhb7


Mass: 30998.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thinopyrum elongatum (tall wheatgrass) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl (pH 8.0), 1.2 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.41→44.84 Å / Num. obs: 22609 / % possible obs: 99.17 % / Redundancy: 7.7 % / Biso Wilson estimate: 40.63 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 17.8
Reflection shellResolution: 2.41→2.501 Å / Rmerge(I) obs: 0.874 / Num. unique obs: 2079

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PHENIX1.19_4092refinement
PHENIX1.19_4092model building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold-prediction

Resolution: 2.41→44.84 Å / SU ML: 0.2487 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.083
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2252 2010 8.9 %
Rwork0.188 20576 -
obs0.1914 22586 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.59 Å2
Refinement stepCycle: LAST / Resolution: 2.41→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3223 0 0 108 3331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863300
X-RAY DIFFRACTIONf_angle_d1.18044489
X-RAY DIFFRACTIONf_chiral_restr0.0681500
X-RAY DIFFRACTIONf_plane_restr0.0099580
X-RAY DIFFRACTIONf_dihedral_angle_d7.3415450
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.04132598817 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.470.30471250.25031323X-RAY DIFFRACTION90.22
2.47-2.540.27161470.23321481X-RAY DIFFRACTION100
2.54-2.620.26711460.23421428X-RAY DIFFRACTION100
2.62-2.70.31441430.22051462X-RAY DIFFRACTION100
2.7-2.80.27151380.20811468X-RAY DIFFRACTION99.94
2.8-2.910.24871510.19911456X-RAY DIFFRACTION100
2.91-3.040.25131330.19761474X-RAY DIFFRACTION100
3.04-3.20.25751490.20361486X-RAY DIFFRACTION100
3.2-3.40.21581420.20151472X-RAY DIFFRACTION100
3.4-3.670.26931420.18411472X-RAY DIFFRACTION100
3.67-4.030.19331450.16821492X-RAY DIFFRACTION100
4.03-4.620.1771560.16021485X-RAY DIFFRACTION100
4.62-5.810.21611450.16581515X-RAY DIFFRACTION100
5.82-44.840.18991480.1881562X-RAY DIFFRACTION98.56

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