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Yorodumi- PDB-2fvl: Crystal structure of human 3-alpha hydroxysteroid/dihydrodiol deh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fvl | ||||||
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Title | Crystal structure of human 3-alpha hydroxysteroid/dihydrodiol dehydrogenase (AKR1C4) complexed with NADP+ | ||||||
Components | Aldo-keto reductase family 1, member C4 | ||||||
Keywords | OXIDOREDUCTASE / Chlordecone reductase / aldo-keto reductase / 3alpha-HSD1 / DD4 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information chlordecone reductase / chlordecone reductase activity / steroid dehydrogenase activity / C21-steroid hormone metabolic process / bile acid transmembrane transporter activity / alcohol dehydrogenase (NADP+) activity / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / androsterone dehydrogenase activity / ketosteroid monooxygenase activity ...chlordecone reductase / chlordecone reductase activity / steroid dehydrogenase activity / C21-steroid hormone metabolic process / bile acid transmembrane transporter activity / alcohol dehydrogenase (NADP+) activity / 3alpha-hydroxysteroid 3-dehydrogenase / cellular response to jasmonic acid stimulus / androsterone dehydrogenase activity / ketosteroid monooxygenase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / bile acid biosynthetic process / aldo-keto reductase (NADPH) activity / bile acid and bile salt transport / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / daunorubicin metabolic process / doxorubicin metabolic process / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / bile acid binding / retinal dehydrogenase activity / aldose reductase (NADPH) activity / retinoid metabolic process / prostaglandin metabolic process / steroid metabolic process / androgen metabolic process / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Retinoid metabolism and transport / steroid binding / oxidoreductase activity / electron transfer activity / extracellular exosome / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Ugochukwu, E. / Smee, C. / Guo, K. / Lukacik, P. / Kavanagh, K. / Debreczeni, J.E. / von Delft, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. ...Ugochukwu, E. / Smee, C. / Guo, K. / Lukacik, P. / Kavanagh, K. / Debreczeni, J.E. / von Delft, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of human 3-alpha hydroxysteroid/dihydrodiol dehydrogenase (AKR1C4) complexed with NADP+ Authors: Ugochukwu, E. / Smee, C. / Guo, K. / Lukacik, P. / Kavanagh, K. / Debreczeni, J.E. / von Delft, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fvl.cif.gz | 225.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fvl.ent.gz | 181.2 KB | Display | PDB format |
PDBx/mmJSON format | 2fvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fvl_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2fvl_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2fvl_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 2fvl_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/2fvl ftp://data.pdbj.org/pub/pdb/validation_reports/fv/2fvl | HTTPS FTP |
-Related structure data
Related structure data | 1xf0S 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 37289.930 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AKR1C4 / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: GenBank: 18088446, UniProt: P17516*PLUS, chlordecone reductase, 3alpha-hydroxysteroid 3-dehydrogenase (Si-specific) #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: 5.999597 Å3/Da / Density % sol: 79.498619 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: Potassium Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→196.12 Å / Num. obs: 104763 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.4→2.53 Å / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XF0.pdb Resolution: 2.4→32.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.982 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Some unexplained positive fofc density was found near to the following residues: - His117 A, B, C; - Lys247 A, B, C; - Arg301 A, B, C
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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 mean: 26.205 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→32.73 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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