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- PDB-7xwh: structure of patulin-detoxifying enzyme with NADP+ -

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Basic information

Entry
Database: PDB / ID: 7xwh
Titlestructure of patulin-detoxifying enzyme with NADP+
ComponentsShort-chain dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / dehydrogenases/reductase
Function / homology: / alcohol dehydrogenase / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / nucleotide binding / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Short-chain dehydrogenase/reductase
Function and homology information
Biological speciesMeyerozyma guilliermondii (fungus)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.31 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 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / 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)115,2578
Polymers112,2834
Non-polymers2,9744
Water11,313628
1
A: Short-chain dehydrogenase/reductase
D: Short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6284
Polymers56,1422
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-26 kcal/mol
Surface area17200 Å2
MethodPISA
2
B: Short-chain dehydrogenase/reductase
C: Short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6284
Polymers56,1422
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-26 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.358, 64.927, 88.984
Angle α, β, γ (deg.)90.000, 107.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Short-chain dehydrogenase/reductase


Mass: 28070.781 Da / Num. of mol.: 4
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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 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: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.31→35.6 Å / Num. obs: 41102 / % possible obs: 99.1 % / Redundancy: 2.84 % / Rmerge(I) obs: 0.0114 / Net I/σ(I): 5.78
Reflection shellResolution: 2.31→2.35 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 2024 / % possible all: 95.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 2.31→35.6 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.716 / SU ML: 0.23 / SU R Cruickshank DPI: 0.4398 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1998 4.9 %RANDOM
Rwork0.1861 ---
obs0.1904 38467 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.19 Å2 / Biso mean: 25.413 Å2 / Biso min: 6.72 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å2-0 Å21.06 Å2
2---1.68 Å20 Å2
3----1.08 Å2
Refinement stepCycle: final / Resolution: 2.31→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6876 0 192 628 7696
Biso mean--52.68 27.49 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137220
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176718
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.6829818
X-RAY DIFFRACTIONr_angle_other_deg1.2711.59115633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4285880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69823.981319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.214151207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9961524
X-RAY DIFFRACTIONr_chiral_restr0.0720.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021452
LS refinement shellResolution: 2.31→2.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 128 -
Rwork0.239 2726 -
all-2854 -
obs--95.61 %

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