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- PDB-5z6t: Crystal structure of D-xylose reductase from Scheffersomyces stip... -

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Basic information

Entry
Database: PDB / ID: 5z6t
TitleCrystal structure of D-xylose reductase from Scheffersomyces stipitis in complex with NADPH
ComponentsNAD(P)H-dependent D-xylose reductase
KeywordsOXIDOREDUCTASE / Pentose metabolism / xylose reductase / Scheffersomyces stipitis
Function / homology
Function and homology information


D-xylose reductase [NAD(P)H] / D-xylose reductase (NADPH) activity / D-xylose catabolic process
Similarity search - Function
Aldo-keto reductase family 2B / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 2B / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD(P)H-dependent D-xylose reductase
Similarity search - Component
Biological speciesScheffersomyces stipitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSon, H.F. / Kim, K.J.
CitationJournal: Sci Rep / Year: 2018
Title: Structural insight intoD-xylose utilization by xylose reductase from Scheffersomyces stipitis
Authors: Son, H.F. / Lee, S.M. / Kim, K.J.
History
DepositionJan 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD(P)H-dependent D-xylose reductase
B: NAD(P)H-dependent D-xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7574
Polymers78,2712
Non-polymers1,4872
Water6,521362
1
A: NAD(P)H-dependent D-xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8792
Polymers39,1351
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-4 kcal/mol
Surface area13400 Å2
MethodPISA
2
B: NAD(P)H-dependent D-xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8792
Polymers39,1351
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-3 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.654, 97.654, 160.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein NAD(P)H-dependent D-xylose reductase / XR


Mass: 39135.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (fungus)
Strain: ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545 / Gene: XYL1, PICST_89614 / Plasmid: pProEX-HTa / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): T1R / References: UniProt: P31867, D-xylose reductase [NAD(P)H]
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 2, 2016
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→83.38 Å / Num. obs: 49336 / % possible obs: 98.6 % / Redundancy: 8.7 % / Rsym value: 0.273 / Net I/σ(I): 26.3
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 2503 / Rsym value: 0.273

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z9A

1z9a


Resolution: 2→83.37 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.235 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.153
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 2658 5.1 %RANDOM
Rwork0.1775 ---
obs0.1799 49336 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.13 Å2 / Biso mean: 29.337 Å2 / Biso min: 10.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å2-0 Å2
2--0.59 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: final / Resolution: 2→83.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5068 0 96 362 5526
Biso mean--38.84 34.14 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195302
X-RAY DIFFRACTIONr_bond_other_d0.0020.025012
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.9827214
X-RAY DIFFRACTIONr_angle_other_deg1.076311558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4275632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.89624.553246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37415878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5671526
X-RAY DIFFRACTIONr_chiral_restr0.1180.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215916
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021222
LS refinement shellResolution: 2.004→2.056 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 184 -
Rwork0.249 3446 -
all-3630 -
obs--95.13 %

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