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- PDB-7xwk: structure of patulin-detoxifying enzyme Y155F with NADPH and substrate -

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Basic information

Entry
Database: PDB / ID: 7xwk
Titlestructure of patulin-detoxifying enzyme Y155F with NADPH and substrate
ComponentsShort-chain dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / dehydrogenases/reductase
Function / homology
Function and homology information


alcohol dehydrogenase / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
: / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-I8L / Chem-NDP / Short-chain dehydrogenase/reductase
Similarity search - Component
Biological speciesMeyerozyma guilliermondii (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsDai, L. / Li, H. / Hu, Y. / Guo, R.T. / Chen, C.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Structure-based rational design of a short-chain dehydrogenase/reductase for improving activity toward mycotoxin patulin.
Authors: Dai, L. / Li, H. / Huang, J.W. / Hu, Y. / He, M. / Yang, Y. / Min, J. / Guo, R.T. / Chen, C.C.
History
DepositionMay 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 8, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase
B: Short-chain dehydrogenase/reductase
C: Short-chain dehydrogenase/reductase
D: Short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,33514
Polymers109,4284
Non-polymers3,90610
Water11,458636
1
A: Short-chain dehydrogenase/reductase
D: Short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6677
Polymers54,7142
Non-polymers1,9535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-26 kcal/mol
Surface area17440 Å2
MethodPISA
2
B: Short-chain dehydrogenase/reductase
C: Short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6677
Polymers54,7142
Non-polymers1,9535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-27 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.333, 65.090, 89.494
Angle α, β, γ (deg.)90.000, 107.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Short-chain dehydrogenase/reductase


Mass: 27357.078 Da / Num. of mol.: 4 / Mutation: Y155F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meyerozyma guilliermondii (fungus) / Gene: SDR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A888VSF1, alcohol dehydrogenase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-I8L / (4~{S})-4-oxidanyl-4,6-dihydrofuro[3,2-c]pyran-2-one


Mass: 154.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 22-23% PEG Smear Broad, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Aug 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.12→35.28 Å / Num. obs: 53451 / % possible obs: 99.9 % / Redundancy: 6.58 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 0.4457
Reflection shellResolution: 2.12→2.15 Å / Rmerge(I) obs: 0.4457 / Num. unique obs: 2199

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XWI

7xwi


Resolution: 2.12→35.28 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.438 / SU ML: 0.19 / SU R Cruickshank DPI: 0.2724 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 2779 5.2 %RANDOM
Rwork0.1965 ---
obs0.2003 50294 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.95 Å2 / Biso mean: 22.959 Å2 / Biso min: 6.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20.17 Å2
2---1.27 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 2.12→35.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6920 0 258 636 7814
Biso mean--50.84 28.41 -
Num. residues----894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137338
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176776
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.6619980
X-RAY DIFFRACTIONr_angle_other_deg1.3361.58115792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1775886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75924.037322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.804151214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6361524
X-RAY DIFFRACTIONr_chiral_restr0.0730.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028028
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021438
LS refinement shellResolution: 2.12→2.175 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 189 -
Rwork0.277 3541 -
all-3730 -
obs--94.43 %

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