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- PDB-1z9a: Crystal Structure Of The Asn-309 To Asp Mutant Of Candida Tenuis ... -

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Basic information

Entry
Database: PDB / ID: 1z9a
TitleCrystal Structure Of The Asn-309 To Asp Mutant Of Candida Tenuis Xylose Reductase (Akr2B5) Bound To Nad+
ComponentsNAD(P)H-dependent D-xylose reductase
KeywordsOXIDOREDUCTASE / beta-alpha-barrel / AKR / aldo-keto reductase / xylose reductase / candida tenuis / substrate selectivity / ketone reduction / structure-activity correlation
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 / isomorphous / Resolution: 2.4 Å
AuthorsKratzer, R. / Leitgeb, S. / Wilson, D.K. / Nidetzky, B.
CitationJournal: Biochem.J. / Year: 2006
Title: Probing the substrate binding site of Candida tenuis xylose reductase (AKR2B5) with site-directed mutagenesis
Authors: Kratzer, R. / Leitgeb, S. / Wilson, D.K. / Nidetzky, B.
History
DepositionApr 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

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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)146,3828
Polymers143,7284
Non-polymers2,6544
Water14,214789
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)73,1914
Polymers71,8642
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-30 kcal/mol
Surface area24320 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)73,1914
Polymers71,8642
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-28 kcal/mol
Surface area24430 Å2
MethodPISA
3
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)146,3828
Polymers143,7284
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1,-z+11
Buried area11120 Å2
ΔGint-63 kcal/mol
Surface area47260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.635, 128.401, 80.004
Angle α, β, γ (deg.)90.00, 90.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2509-

HOH

21D-4351-

HOH

31D-4493-

HOH

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Components

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


Mass: 35931.992 Da / Num. of mol.: 4 / Mutation: N310D
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): BL21(DE3)
References: UniProt: O74237, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: ammonium sulfate, sodium acetate, sodium citrate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jan 28, 2004
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 64303 / Num. obs: 64303 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.17
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.2 / % possible all: 82.9

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: isomorphous
Starting model: candida tenuis xylose reductase bound to nad

Resolution: 2.4→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3160 -randomly
Rwork0.176 ---
obs0.176 64105 90 %-
all-64105 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.409 Å20 Å2-7.955 Å2
2--6.091 Å20 Å2
3----1.682 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10128 0 176 789 11093
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007421
X-RAY DIFFRACTIONc_angle_d1.35163
X-RAY DIFFRACTIONc_mcbond_it1.7821.5
X-RAY DIFFRACTIONc_mcangle_it2.6422
X-RAY DIFFRACTIONc_scbond_it2.8132
X-RAY DIFFRACTIONc_scangle_it3.7592.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5par.nad_xrtop.nad_xr

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