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- PDB-1ye6: Crystal structure of the Lys-274 to Arg mutant of Candida tenuis ... -

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Basic information

Entry
Database: PDB / ID: 1ye6
TitleCrystal structure of the Lys-274 to Arg mutant of Candida tenuis xylose reductase (AKR2B5) bound to NADP+
ComponentsNAD(P)H-dependent D-xylose reductase
KeywordsOXIDOREDUCTASE / beta-alpha-barrel AKR aldo-keto reductase coenzyme specificity NADP
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD(P)H-dependent D-xylose reductase
Similarity search - Component
Biological speciesCandida tenuis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomourphous / Resolution: 2.3 Å
AuthorsLeitgeb, S. / Petschacher, B. / Wilson, D.K. / Nidetzky, B.
CitationJournal: Febs Lett. / Year: 2005
Title: Fine tuning of coenzyme specificity in family 2 aldo-keto reductases revealed by crystal structures of the Lys-274-->Arg mutant of Candida tenuis xylose reductase (AKR2B5) bound to NAD(+) and NADP(+).
Authors: Leitgeb, S. / Petschacher, B. / Wilson, D.K. / Nidetzky, B.
History
DepositionDec 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: NAD(P)H-dependent D-xylose reductase
D: NAD(P)H-dependent D-xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,94316
Polymers144,3614
Non-polymers3,58212
Water13,691760
1
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)73,9728
Polymers72,1802
Non-polymers1,7916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-64 kcal/mol
Surface area24600 Å2
MethodPISA
2
C: NAD(P)H-dependent D-xylose reductase
D: NAD(P)H-dependent D-xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9728
Polymers72,1802
Non-polymers1,7916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-65 kcal/mol
Surface area24570 Å2
MethodPISA
3
A: NAD(P)H-dependent D-xylose reductase
B: NAD(P)H-dependent D-xylose reductase
hetero molecules

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

C: NAD(P)H-dependent D-xylose reductase
D: NAD(P)H-dependent D-xylose reductase
hetero molecules

C: NAD(P)H-dependent D-xylose reductase
D: NAD(P)H-dependent D-xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,88632
Polymers288,7228
Non-polymers7,16424
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_646-x+1,y-1,-z+11
Buried area28320 Å2
ΔGint-270 kcal/mol
Surface area91890 Å2
MethodPISA
4
A: NAD(P)H-dependent D-xylose reductase
B: NAD(P)H-dependent D-xylose reductase
hetero molecules

C: NAD(P)H-dependent D-xylose reductase
D: NAD(P)H-dependent D-xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,94316
Polymers144,3614
Non-polymers3,58212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1,-z+11
Buried area12650 Å2
ΔGint-137 kcal/mol
Surface area47450 Å2
MethodPISA
5
A: NAD(P)H-dependent D-xylose reductase
B: NAD(P)H-dependent D-xylose reductase
hetero molecules

C: NAD(P)H-dependent D-xylose reductase
D: NAD(P)H-dependent D-xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,94316
Polymers144,3614
Non-polymers3,58212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544x+1/2,y-1/2,z-11
Buried area11670 Å2
ΔGint-134 kcal/mol
Surface area48440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.005, 127.988, 80.074
Angle α, β, γ (deg.)90.00, 90.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1045-

HOH

21D-1059-

HOH

31D-1093-

HOH

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Components

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


Mass: 36090.215 Da / Num. of mol.: 4 / Mutation: K274R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tenuis (fungus) / Gene: XYL1, XYLR / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21(DE3)
References: UniProt: O74237, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 760 / 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: 3.19 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: Ammonium sulfate, sodium citrate, sodium acetate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.953695 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2004
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953695 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 80204 / Num. obs: 80204 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.38
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4.47 / % possible all: 98.8

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: isomourphous
Starting model: PDB-entry 1K8C

1k8c


Resolution: 2.3→30 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3921 4.9 %Randomly
Rwork0.192 ---
obs0.192 80192 99.7 %-
all-80192 --
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10132 0 224 760 11116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.25459
X-RAY DIFFRACTIONc_bond_d0.005953

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