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- PDB-7y9p: Xylitol dehydrogenase S96C/S99C/Y102C mutant(thermostabilized for... -

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Basic information

Entry
Database: PDB / ID: 7y9p
TitleXylitol dehydrogenase S96C/S99C/Y102C mutant(thermostabilized form) from Pichia stipitis
ComponentsXylitol dehydrogenase
KeywordsOXIDOREDUCTASE / Xylitol / Medium chain dehydrogenase/reductase family / structural zinc atom
Function / homology
Function and homology information


D-xylulose reductase / D-xylulose reductase activity / zinc ion binding
Similarity search - Function
Sorbitol dehydrogenase-like / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Xylitol dehydrogenase
Similarity search - Component
Biological speciesScheffersomyces stipitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYoshiwara, K. / Watanabe, Y. / Watanabe, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2023
Title: Molecular evolutionary insight of structural zinc atom in yeast xylitol dehydrogenases and its application in bioethanol production by lignocellulosic biomass.
Authors: Yoshiwara, K. / Watanabe, S. / Watanabe, Y.
History
DepositionJun 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2346
Polymers39,8091
Non-polymers4255
Water27015
1
A: Xylitol dehydrogenase
hetero molecules

A: Xylitol dehydrogenase
hetero molecules

A: Xylitol dehydrogenase
hetero molecules

A: Xylitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,93824
Polymers159,2374
Non-polymers1,70020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z1
crystal symmetry operation12_565x,x-y+1,-z1
Buried area12470 Å2
ΔGint-244 kcal/mol
Surface area51920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.272, 158.272, 65.497
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Xylitol dehydrogenase


Mass: 39809.336 Da / Num. of mol.: 1 / Mutation: S96C, S99C, Y102C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis (fungus) / Gene: Xyl2 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: E5G6H4

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Non-polymers , 5 types, 20 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.0, 2.5%(w/v) PEG400, 2.0 M ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.8→47.35 Å / Num. obs: 22638 / % possible obs: 100 % / Redundancy: 57.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.457 / Rpim(I) all: 0.061 / Rrim(I) all: 0.461 / Χ2: 1 / Net I/σ(I): 16.6
Reflection shellResolution: 2.8→2.95 Å / % possible obs: 100 % / Redundancy: 60.5 % / Rmerge(I) obs: 4.19 / Num. measured all: 106523 / Num. unique obs: 1762 / CC1/2: 0.856 / Rpim(I) all: 0.544 / Rrim(I) all: 4.226 / Χ2: 0.98 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDS0.7.4data scaling
PDB_EXTRACT3.27data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QE3

3qe3


Resolution: 2.8→47.35 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.274 1130 4.99 %
Rwork0.2229 --
obs0.2253 22638 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 20 15 2653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042694
X-RAY DIFFRACTIONf_angle_d0.6883664
X-RAY DIFFRACTIONf_dihedral_angle_d6.543376
X-RAY DIFFRACTIONf_chiral_restr0.048419
X-RAY DIFFRACTIONf_plane_restr0.005479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.36711430.34292689X-RAY DIFFRACTION100
2.93-3.080.40621400.32842689X-RAY DIFFRACTION100
3.08-3.270.37011370.30062695X-RAY DIFFRACTION100
3.28-3.530.36891600.2492655X-RAY DIFFRACTION100
3.53-3.880.29871510.23812693X-RAY DIFFRACTION100
3.88-4.440.25641180.19572691X-RAY DIFFRACTION100
4.44-5.590.18331110.19142717X-RAY DIFFRACTION100
5.6-47.350.22751700.18112679X-RAY DIFFRACTION100

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