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- PDB-8k2o: Crystal structure of Fhb7-M10 -

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Basic information

Entry
Database: PDB / ID: 8k2o
TitleCrystal structure of Fhb7-M10
ComponentsFhb7-M10
KeywordsTRANSFERASE / Fhb7 / Detoxification / Deoxynivalenol
Biological speciesThinopyrum elongatum (tall wheatgrass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsYang, J. / Lei, X.G. / Xiao, J.Y.
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
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: Fhb7-M10
B: Fhb7-M10
C: Fhb7-M10
D: Fhb7-M10


Theoretical massNumber of molelcules
Total (without water)126,0124
Polymers126,0124
Non-polymers00
Water12,394688
1
A: Fhb7-M10


Theoretical massNumber of molelcules
Total (without water)31,5031
Polymers31,5031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fhb7-M10


Theoretical massNumber of molelcules
Total (without water)31,5031
Polymers31,5031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fhb7-M10


Theoretical massNumber of molelcules
Total (without water)31,5031
Polymers31,5031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fhb7-M10


Theoretical massNumber of molelcules
Total (without water)31,5031
Polymers31,5031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.506, 112.156, 135.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Fhb7-M10


Mass: 31502.957 Da / Num. of mol.: 4
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.: 688 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% PEG 3350

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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: 2.01→67.59 Å / Num. obs: 79602 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.033 / Rrim(I) all: 0.114 / Χ2: 0.88 / Net I/σ(I): 16.9 / Num. measured all: 945516
Reflection shellResolution: 2.01→2.11 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.057 / Num. unique obs: 11470 / CC1/2: 0.804 / Rpim(I) all: 0.328 / Rrim(I) all: 0.114 / Χ2: 0.72

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YOC

7yoc


Resolution: 2.01→51.8 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 1998 2.51 %
Rwork0.1999 --
obs0.2007 79493 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→51.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8343 0 0 688 9031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d6.0231179
X-RAY DIFFRACTIONf_chiral_restr0.051263
X-RAY DIFFRACTIONf_plane_restr0.011523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.060.30361400.25955457X-RAY DIFFRACTION100
2.06-2.110.30271420.245475X-RAY DIFFRACTION100
2.11-2.170.24571390.23025446X-RAY DIFFRACTION100
2.17-2.240.2691410.22385501X-RAY DIFFRACTION100
2.24-2.320.2561410.22195462X-RAY DIFFRACTION100
2.32-2.420.30171420.21855508X-RAY DIFFRACTION100
2.42-2.530.25591430.2175499X-RAY DIFFRACTION100
2.53-2.660.28641420.22285516X-RAY DIFFRACTION100
2.66-2.830.2731420.22035511X-RAY DIFFRACTION100
2.83-3.050.25011430.21375535X-RAY DIFFRACTION100
3.05-3.350.22921430.20375533X-RAY DIFFRACTION100
3.35-3.840.22661440.18965600X-RAY DIFFRACTION100
3.84-4.830.19741460.16545628X-RAY DIFFRACTION100
4.84-51.80.17911500.1815824X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -2.2642 Å / Origin y: -13.5486 Å / Origin z: -37.0535 Å
111213212223313233
T0.2075 Å20.0289 Å2-0.0119 Å2-0.1674 Å2-0.0373 Å2--0.2141 Å2
L0.3697 °20.1125 °2-0.1229 °2-0.075 °2-0.0277 °2--0.2329 °2
S0.0005 Å °-0.0393 Å °-0.0307 Å °0.001 Å °0.0044 Å °0.0055 Å °0.006 Å °0.0187 Å °0 Å °
Refinement TLS groupSelection details: all

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