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- PDB-1k8c: Crystal structure of dimeric xylose reductase in complex with NADP(H) -

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Basic information

Entry
Database: PDB / ID: 1k8c
TitleCrystal structure of dimeric xylose reductase in complex with NADP(H)
Componentsxylose reductase
KeywordsOXIDOREDUCTASE / beta-alpha barrel / aldo-keto reductase / NADP(H)
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 speciesCandida tenuis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionOct 23, 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 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)147,2228
Polymers144,2494
Non-polymers2,9744
Water13,223734
1
A: xylose reductase
B: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6114
Polymers72,1242
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-21 kcal/mol
Surface area24250 Å2
MethodPISA
2
C: xylose reductase
D: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6114
Polymers72,1242
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-21 kcal/mol
Surface area24150 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)147,2228
Polymers144,2494
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_547-x+1/2,y-1/2,-z+21
Buried area11470 Å2
ΔGint-47 kcal/mol
Surface area46870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.202, 127.809, 80.251
Angle α, β, γ (deg.)90.00, 90.37, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2583-

HOH

21B-2584-

HOH

31C-3542-

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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


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


Mass: 18.015 Da / Num. of mol.: 734 / 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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, ammonium sulfate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 293K, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 mg/mlprotein1drop
25 mMNADPH1drop
310 mMHEPES1droppH7.4
432 %(w/v)PEG5000 MME1reservoir
5300 mMammonium sulfate1reservoir
6100 mMsodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 106917 / Num. obs: 105789 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.082
Reflection shellResolution: 2.1→2.14 Å / % possible all: 98
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Num. obs: 93492 / % possible obs: 99.5 % / Num. measured all: 325247 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.24 Å / % possible obs: 98.7 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo xylose reductase

Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 5269 5 %random
Rwork0.213 ---
all-106917 --
obs-105789 --
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10111 0 192 734 11037
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_bond_d0.009
LS refinement shellResolution: 2.1→2.14 Å / Num. reflection obs: 5247
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 92623 / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.208 / Highest resolution: 2.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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