+Open data
-Basic information
Entry | Database: PDB / ID: 3o3r | ||||||
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Title | Crystal Structure of AKR1B14 in complex with NADP | ||||||
Components | Aldo-keto reductase family 1, member B7 | ||||||
Keywords | OXIDOREDUCTASE / Aldose reductase like protein / AKR1B14 | ||||||
Function / homology | Function and homology information Estrogen biosynthesis / aldo-keto reductase (NADPH) activity / aldose reductase / prostaglandin H2 endoperoxidase reductase activity / aldose reductase (NADPH) activity / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å | ||||||
Authors | Sundaram, K. / Dhagat, U. / El-Kabbani, O. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Structure of rat aldose reductase-like protein AKR1B14 holoenzyme: Probing the role of His269 in coenzyme binding by site-directed mutagenesis Authors: Sundaram, K. / Dhagat, U. / Endo, S. / Chung, R. / Matsunaga, T. / Hara, A. / El-Kabbani, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o3r.cif.gz | 153.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o3r.ent.gz | 119.7 KB | Display | PDB format |
PDBx/mmJSON format | 3o3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/3o3r ftp://data.pdbj.org/pub/pdb/validation_reports/o3/3o3r | HTTPS FTP |
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-Related structure data
Related structure data | 1pwlS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36173.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pCold IV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5RJP0 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.79 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 20% polyethylene glycol 4000, 10% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 7, 2010 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→30 Å / Num. all: 50520 / Num. obs: 49358 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.48 % / Rmerge(I) obs: 0.0477 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 3.02 % / Rmerge(I) obs: 0.2796 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4018 / % possible all: 90.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PWL Resolution: 1.86→28.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2536 / WRfactor Rwork: 0.1892 / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8216 / SU B: 3.85 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1742 / SU Rfree: 0.1656 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.21 Å2 / Biso mean: 27.0707 Å2 / Biso min: 8.06 Å2
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Refine analyze | Luzzati coordinate error obs: 0.208 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→28.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.862→1.93 Å / Total num. of bins used: 20
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