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- PDB-1cwn: CRYSTAL STRUCTURE OF PORCINE ALDEHYDE REDUCTASE HOLOENZYME -

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Basic information

Entry
Database: PDB / ID: 1cwn
TitleCRYSTAL STRUCTURE OF PORCINE ALDEHYDE REDUCTASE HOLOENZYME
ComponentsALDEHYDE REDUCTASEAldose reductase
KeywordsOXIDOREDUCTASE / TIM-BARREL / NADP
Function / homologyNADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain superfamily / Aldo/keto reductase / Aldo/keto reductase, conserved site / Aldo/keto reductase family / Aldo/keto reductase family signature 2. / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Glutathione conjugation / Formation of xylulose-5-phosphate ...NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain superfamily / Aldo/keto reductase / Aldo/keto reductase, conserved site / Aldo/keto reductase family / Aldo/keto reductase family signature 2. / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Glutathione conjugation / Formation of xylulose-5-phosphate / mevaldate reductase (NADPH) / D/L-glyceraldehyde reductase / glucuronolactone reductase / glucuronate reductase / D-glucuronate catabolic process / alcohol dehydrogenase (NADP+) / L-ascorbic acid biosynthetic process / aldehyde catabolic process / cellular detoxification of aldehyde / allyl-alcohol dehydrogenase / alditol:NADP+ 1-oxidoreductase activity / alcohol dehydrogenase (NADP+) activity / oxidoreductase activity / cytosol / Aldo-keto reductase family 1 member A1
Function and homology information
Specimen sourceSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsEl-Kabbani, O.
Citation
Journal: Protein Pept.Lett. / Year: 1996
Title: Crystal structure of porcine aldehyde reductase at 2.0 angstrom resolution: Modeling an inhibitor in the active site of the enzyme.
Authors: ElKabbani, O. / Carper, D.A. / McGowan, M.H. / Ginell, S.L.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure of Porcine Aldehyde Reductase Holoenzyme
Authors: El-Kabbani, O. / Judge, K. / Ginell, S.L. / Myles, D.A. / Delucas, L.J. / Flynn, T.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 30, 1996 / Release: Feb 4, 1998
RevisionDateData content typeGroupProviderType
1.0Feb 4, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALDEHYDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1962
Polyers36,4531
Non-polymers7431
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)67.200, 67.200, 243.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP 65 2 2

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Components

#1: Protein/peptide ALDEHYDE REDUCTASE / Aldose reductase / ALR1 / Coordinate model: Cα atoms only


Mass: 36452.691 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa (pig) / Organ: KIDNEY / Tissue: MEDULLA, CORTEX / References: UniProt: P50578, alcohol dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Formula: C21H28N7O17P3 / Nicotinamide adenine dinucleotide phosphate

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 45 %

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.00615
DetectorDetector: CCD / Date: Jun 15, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00615 Å / Relative weight: 1
ReflectionNum. obs: 21648 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.03

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Processing

Software
NameClassification
X-PLORrefinement
MADNESdata reduction
RefinementResolution: 2→6 Å / σ(F): 4 /
RfactorNum. reflection
Rwork0.2-
obs0.220127
Displacement parametersBiso mean: 16.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms3240480372
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
x_bond_d0.009
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg2.3
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it1.5
x_mcangle_it2
x_scbond_it2
x_scangle_it2.5

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