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- PDB-1mi3: 1.8 Angstrom structure of xylose reductase from Candida tenuis in... -

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Basic information

Entry
Database: PDB / ID: 1mi3
Title1.8 Angstrom structure of xylose reductase from Candida tenuis in complex with NAD
Componentsxylose reductase
KeywordsOXIDOREDUCTASE / aldo-keto reductase / beta-alpha barrel / dimer
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD(P)H-dependent D-xylose reductase
Similarity search - Component
Biological speciesCandida tenuis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKavanagh, K.L. / Klimacek, M. / Nidetzky, B. / Wilson, D.K.
CitationJournal: Biochem.J. / Year: 2003
Title: Structure of xylose reductase bound to NAD+ and the basis for single and dual co-substrate specificity in family 2 aldo-keto reductases
Authors: Kavanagh, K.L. / Klimacek, M. / Nidetzky, B. / Wilson, D.K.
History
DepositionAug 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2013Group: Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: xylose reductase
B: xylose reductase
C: xylose reductase
D: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,9028
Polymers144,2494
Non-polymers2,6544
Water15,727873
1
A: xylose reductase
B: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4514
Polymers72,1242
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-28 kcal/mol
Surface area24400 Å2
MethodPISA
2
C: xylose reductase
D: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4514
Polymers72,1242
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-26 kcal/mol
Surface area24390 Å2
MethodPISA
3
A: xylose reductase
B: xylose reductase
hetero molecules

C: xylose reductase
D: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,9028
Polymers144,2494
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1,-z+11
Buried area11190 Å2
ΔGint-60 kcal/mol
Surface area47290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.202, 128.344, 79.949
Angle α, β, γ (deg.)90.00, 90.75, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2400-

HOH

21B-2472-

HOH

31D-4408-

HOH

41D-4492-

HOH

51D-4522-

HOH

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Components

#1: Protein
xylose reductase / E.C.1.1.1.21 / NAD(P)H-DEPENDENT XYLOSE REDUCTASE / XR


Mass: 36062.199 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tenuis (fungus) / Gene: xylR / Plasmid: pBEAct.1i / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O74237, aldose reductase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 873 / 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: 2.95 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 32% PEG-ME 5K, 350 mM ammonium sulfate, 100 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
22.5 mMNAD+1drop
316 %(w/v)PEG5000 MME1drop
4175 mMammonium sulfate1drop
550 mMsodium citrate1droppH5.6
632 %(w/v)PEG5000 MME1reservoir
7350 mMammonium sulfate1reservoir
8100 mMsodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 164527 / Num. obs: 162718 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3 / % possible all: 98.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 162716 / Num. measured all: 728917
Reflection shell
*PLUS
% possible obs: 98.2 % / Mean I/σ(I) obs: 3.02

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished model of XR mutant

Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 8175 -random
Rwork0.1828 ---
all0.1828 167717 --
obs0.1828 162716 5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.979 Å20 Å2-4.544 Å2
2--2.304 Å20 Å2
3----1.324 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10128 0 176 873 11177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.71
X-RAY DIFFRACTIONc_bond_d0.018
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. reflection obs: 154541 / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.7

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