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- PDB-1pyf: Structure of NADPH-dependent family 11 aldo-keto reductase AKR11A(apo) -

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Basic information

Entry
Database: PDB / ID: 1pyf
TitleStructure of NADPH-dependent family 11 aldo-keto reductase AKR11A(apo)
ComponentsIolS protein
KeywordsOXIDOREDUCTASE / beta-alpha barrel / aldo-keto reductase / TIM barrel
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / cytosol
Similarity search - Function
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
Aldo-keto reductase IolS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsEhrensberger, A.H. / Wilson, D.K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural and Catalytic Diversity in the Two Family 11 Aldo-keto Reductases
Authors: Ehrensberger, A.H. / Wilson, D.K.
History
DepositionJul 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IolS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6594
Polymers35,5121
Non-polymers1473
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.277, 88.101, 94.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsOne monomer forms the biological unit.

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Components

#1: Protein IolS protein / Vegetative protein 147 / VEG147


Mass: 35511.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: IOLS OR SS92ER / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* / References: UniProt: P46336
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.86
Details: PEG 3000, CHES, pH 9.86, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 9.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
146 mg/mlprotein1drop
2100 mMCHES1reservoirpH9.9
332 %(w/v)PEG30001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97903, 0.88558, 0.97922
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 21, 2003 / Details: double crystal
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979031
20.885581
30.979221
ReflectionResolution: 1.8→100 Å / Num. all: 34756 / Num. obs: 34747 / % possible obs: 85.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.6
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.9 / % possible all: 94.7
Reflection
*PLUS
Num. obs: 36324 / % possible obs: 98.8 % / Num. measured all: 158756
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 94.7 % / Rmerge(I) obs: 0.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1721 -RANDOM
Rwork0.197 ---
all0.197 34690 --
obs0.197 34690 94.8 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2488 0 9 241 2738
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.78
X-RAY DIFFRACTIONc_bond_d0.019

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