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- PDB-1jez: THE STRUCTURE OF XYLOSE REDUCTASE, A DIMERIC ALDO-KETO REDUCTASE ... -

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Basic information

Entry
Database: PDB / ID: 1jez
TitleTHE STRUCTURE OF XYLOSE REDUCTASE, A DIMERIC ALDO-KETO REDUCTASE FROM CANDIDA TENUIS
ComponentsXYLOSE REDUCTASE
KeywordsOXIDOREDUCTASE / TIM BARREL / ALDO-KETO REDUCTASE / NADPH / NADH
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
NAD(P)H-dependent D-xylose reductase
Similarity search - Component
Biological speciesCandida tenuis (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKavanagh, K.L. / Klimacek, M. / Nidetzky, B. / Wilson, D.K.
CitationJournal: Biochemistry / Year: 2002
Title: The structure of apo and holo forms of xylose reductase, a dimeric aldo-keto reductase from Candida tenuis.
Authors: Kavanagh, K.L. / Klimacek, M. / Nidetzky, B. / Wilson, D.K.
History
DepositionJun 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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

Downloads & links

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Assembly

Deposited unit
A: XYLOSE REDUCTASE
B: XYLOSE REDUCTASE


Theoretical massNumber of molelcules
Total (without water)72,1242
Polymers72,1242
Non-polymers00
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-15 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.840, 63.350, 103.160
Angle α, β, γ (deg.)90.00, 111.28, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein XYLOSE REDUCTASE / E.C.1.1.1.21


Mass: 36062.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tenuis (fungus) / Gene: XYLR / Plasmid: PBEACT.LI / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O74237, aldose reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG 4000, 200mM ammonium acetate, 100 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
215 %(w/v)PEG40001drop
3100 mMammonium acetate1drop
450 mMsodium citrate1droppH5.6
530 %(w/v)PEG40001reservoir
6200 mMammonium acetate1reservoir
7100 mMsodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 16, 2001 / Details: mirrors
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 33863 / Num. obs: 33457 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.26 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.1 / % possible all: 97.3
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 109237 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 97.3 % / Rmerge(I) obs: 0.406

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Processing

Software
NameClassification
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: modified 1ADS

1ads


Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1581 4.9 %RANDOM
Rwork0.179 ---
all0.179 33973 --
obs0.179 31972 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.925 Å20 Å2-1.03 Å2
2---2.124 Å20 Å2
3---7.049 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 0 407 5177
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008643
X-RAY DIFFRACTIONc_angle_deg1.35383
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.4931.5
X-RAY DIFFRACTIONc_mcangle_it2.1172
X-RAY DIFFRACTIONc_scbond_it2.3782
X-RAY DIFFRACTIONc_scangle_it2.8642.5
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 30391 / Rfactor obs: 0.179 / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.35

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