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Yorodumi- PDB-4fiz: Crystal structure of the binary complex between a fungal 17beta-h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fiz | ||||||
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Title | Crystal structure of the binary complex between a fungal 17beta-hydroxysteroid dehydrogenase (Apo form) and coumestrol | ||||||
Components | 17beta-hydroxysteroid dehydrogenase | ||||||
Keywords | Oxidoreductase/Oxidoreductase inhibitor / Short chain Dehydrogenase/Reductase / Rossmann Fold / Oxidoreductase / NADP(H) / Oxidoreductase-Oxidoreductase inhibitor complex | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on CH-OH group of donors / nucleotide binding Similarity search - Function | ||||||
Biological species | Cochliobolus lunatus (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Cassetta, A. / Lamba, D. / Krastanova, I. | ||||||
Citation | Journal: To be Published Title: Crystallographic studies on the flavonoid inhibition of a fungal 17beta-hydroxysteroid dehydrogenase Authors: Cassetta, A. / Lamba, D. / Krastanova, I. / Kristan, K. / Brunskole-Svegelj, M. / Stojan, J. / Lanisnik-Rizner, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fiz.cif.gz | 123.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fiz.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 4fiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fiz_validation.pdf.gz | 731.6 KB | Display | wwPDB validaton report |
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Full document | 4fiz_full_validation.pdf.gz | 734.6 KB | Display | |
Data in XML | 4fiz_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 4fiz_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/4fiz ftp://data.pdbj.org/pub/pdb/validation_reports/fi/4fiz | HTTPS FTP |
-Related structure data
Related structure data | 3is3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28936.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cochliobolus lunatus (fungus) / Strain: m118 / Gene: 17HSDcl / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): JM107 References: UniProt: O93874, 17beta-estradiol 17-dehydrogenase |
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-Non-polymers , 5 types, 171 molecules
#2: Chemical | ChemComp-CUE / | ||||
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#3: Chemical | ChemComp-DMS / | ||||
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / | #6: 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: 2.67 Å3/Da / Density % sol: 53.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% (W/V) PEG 6000, 20% (V/V) Glycerol, 0.1 M Tris Soaked for 24 hours with: 20% (W/V) PEG 6000, 20% (V/V) Glycerol, 0.1 M Tris 2 mM coumestrol. 5% DMSO in the soaking solution, pH 8.0, ...Details: 20% (W/V) PEG 6000, 20% (V/V) Glycerol, 0.1 M Tris Soaked for 24 hours with: 20% (W/V) PEG 6000, 20% (V/V) Glycerol, 0.1 M Tris 2 mM coumestrol. 5% DMSO in the soaking solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2010 / Details: Platinum coated cylindrical mirror |
Radiation | Monochromator: Double crystal Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 24719 / Num. obs: 24719 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 2.5 % / Rmerge(I) obs: 3.2 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1249 / Rsym value: 0.203 / % possible all: 82.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IS3 Resolution: 1.9→19.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.289 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.813 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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