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- PDB-1sm9: Crystal Structure Of An Engineered K274RN276D Double Mutant of Xy... -

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Basic information

Entry
Database: PDB / ID: 1sm9
TitleCrystal Structure Of An Engineered K274RN276D Double Mutant of Xylose Reductase From Candida Tenuis Optimized To Utilize NAD
Componentsxylose reductase
KeywordsOXIDOREDUCTASE / xylose metabolism / coenzyme specificity / aldo-keto reductase / beta-alpha-barrel / AKR2B5
Function / homology
Function and homology information


D-xylose reductase [NAD(P)H] / D-xylose reductase (NADPH) activity / D-xylose catabolic process / cytosol
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 / isomorphous / Resolution: 2.2 Å
AuthorsPetschacher, B. / Leitgeb, S. / Kavanagh, K.L. / Wilson, D.K. / Nidetzky, B.
CitationJournal: Biochem.J. / Year: 2005
Title: The coenzyme specificity of Candida tenuis xylose reductase (AKR2B5) explored by site-directed mutagenesis and X-ray crystallography.
Authors: Petschacher, B. / Leitgeb, S. / Kavanagh, K.L. / Wilson, D.K. / Nidetzky, B.
History
DepositionMar 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Oct 27, 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 1.6Aug 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: xylose reductase
B: xylose reductase
C: xylose reductase
D: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0188
Polymers144,3654
Non-polymers2,6544
Water14,286793
1
A: xylose reductase
B: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5094
Polymers72,1822
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-28 kcal/mol
Surface area24350 Å2
MethodPISA
2
C: xylose reductase
D: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5094
Polymers72,1822
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-28 kcal/mol
Surface area24310 Å2
MethodPISA
3
A: xylose reductase
B: xylose reductase
hetero molecules

A: xylose reductase
B: xylose reductase
hetero molecules

C: xylose reductase
D: xylose reductase
hetero molecules

C: xylose reductase
D: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,03716
Polymers288,7308
Non-polymers5,3078
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 area25390 Å2
ΔGint-123 kcal/mol
Surface area91210 Å2
MethodPISA
4
A: xylose reductase
B: xylose reductase
hetero molecules

C: xylose reductase
D: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0188
Polymers144,3654
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1,-z+11
Buried area11200 Å2
ΔGint-63 kcal/mol
Surface area47100 Å2
MethodPISA
5
A: xylose reductase
B: xylose reductase
hetero molecules

A: xylose reductase
B: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0188
Polymers144,3654
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11110 Å2
ΔGint-55 kcal/mol
Surface area47220 Å2
MethodPISA
6
C: xylose reductase
D: xylose reductase
hetero molecules

C: xylose reductase
D: xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0188
Polymers144,3654
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11160 Å2
ΔGint-54 kcal/mol
Surface area47110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.74, 128.19, 79.67
Angle α, β, γ (deg.)90.00, 90.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2383-

HOH

21D-4383-

HOH

31D-4584-

HOH

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Components

#1: Protein
xylose reductase


Mass: 36091.199 Da / Num. of mol.: 4 / Mutation: K274R, N276D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tenuis (fungus) / Plasmid: pBEAct.1i / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 3289019, UniProt: O74237*PLUS, 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.: 793 / 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: 3.2 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: ammonium sulfate, sodium acetate, sodium citrate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 11, 2003
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 91362 / Num. obs: 91362 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.51
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: isomorphous
Starting model: wild-type structure of xylose reductase from candida tenuis bound to nad, pdb entry 1MI3

1mi3


Resolution: 2.2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 4476 randomly, 4.9% of data
Rwork0.194 --
obs0.194 91237 -
all-91237 -
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10132 0 176 793 11101
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00917
X-RAY DIFFRACTIONc_angle_deg1.62804

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