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Yorodumi- PDB-3wcz: Crystal structure of Bombyx mori aldo-keto reductase (AKR2E4) in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wcz | ||||||
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Title | Crystal structure of Bombyx mori aldo-keto reductase (AKR2E4) in complex with NADP | ||||||
Components | Aldo-keto reductase 2E | ||||||
Keywords | OXIDOREDUCTASE / TIM-BARREL / REDUCTASE / NADP / CYTOSOL | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / steroid metabolic process / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Bombyx mori (domestic silkworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Yamamoto, K. / Wilson, D.K. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2013 Title: Identification, characterization, and crystal structure of an aldo-keto reductase (AKR2E4) from the silkworm Bombyx mori. Authors: Yamamoto, K. / Wilson, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wcz.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wcz.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wcz_validation.pdf.gz | 728.3 KB | Display | wwPDB validaton report |
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Full document | 3wcz_full_validation.pdf.gz | 730.2 KB | Display | |
Data in XML | 3wcz_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 3wcz_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/3wcz ftp://data.pdbj.org/pub/pdb/validation_reports/wc/3wcz | HTTPS FTP |
-Related structure data
Related structure data | 2hdjS 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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Unit cell |
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-Components
#1: Protein | Mass: 34385.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: akr2e / Production host: Escherichia coli (E. coli) / References: UniProt: H9JTG9 | ||||
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#2: Chemical | ChemComp-NAP / | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CIT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1M SODIUM CITRATE, 0.1M CACODYLATE (PH 6.5), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→34.503 Å / Num. obs: 69041 / % possible obs: 98.5 % / Observed criterion σ(I): 3 |
Reflection shell | Highest resolution: 1.3 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HDJ Resolution: 1.3→34.5 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 16.65 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.17 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45 Å2 / ksol: 0.5 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.3→34.5 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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