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- PDB-1c9w: CHO REDUCTASE WITH NADP+ -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1c9w
TitleCHO REDUCTASE WITH NADP+
ComponentsCHO REDUCTASE
KeywordsOXIDOREDUCTASE / ALPHA/BETA TIM BARREL / PROTEIN-NADP+ COMPLEX
Function / homology
Function and homology information


aldose reductase / aldose reductase (NADPH) activity / cytoplasm
Similarity search - Function
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 ...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 / Aldose reductase-related protein 2
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsYe, Q. / Li, X. / Hyndman, D. / Flynn, T.G. / Jia, Z.
CitationJournal: Proteins / Year: 2000
Title: Crystal structure of CHO reductase, a member of the aldo-keto reductase superfamily.
Authors: Ye, Q. / Hyndman, D. / Li, X. / Flynn, T.G. / Jia, Z.
History
DepositionAug 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHO REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0012
Polymers36,2581
Non-polymers7431
Water5,405300
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.282, 84.282, 120.539
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CHO REDUCTASE


Mass: 36257.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Organ: OVARY / Plasmid: PET16B / Production host: Escherichia coli (E. coli) / References: UniProt: O08782, alcohol dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 3.41 Å3/Da / Density % sol: 63.89 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: PEG 4000, AMMONIUM SULPHATE, 2,5-HEXANEDIOL, pH 6.5, EVAPORATION, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21 mMEDTA1drop
310 mMPIPES1drop
41 mMbeta-mercaptoethanol1drop
549 mMNADP+1drop0.02ml
60.2 MPEG40001reservoir
70.2 Mammonium sulfate1reservoir
80.4 %(v/v)2,5-hexanediol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→2.49 Å / Num. all: 420251 / Num. obs: 19882 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 42.916 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.253 / % possible all: 100
Reflection
*PLUS
Num. measured all: 420251
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1948 -RANDOM
Rwork0.201 ---
all0.201 19917 --
obs0.201 19779 99.3 %-
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 48 300 2903
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00639
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.198
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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