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Yorodumi- PDB-3nbr: Crystal Structure of Ketosteroid Isomerase D38NP39GD99N from Pseu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nbr | ||||||
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Title | Crystal Structure of Ketosteroid Isomerase D38NP39GD99N from Pseudomonas Testosteroni (tKSI) with 4-Androstene-3,17-dione Bound | ||||||
Components | Steroid Delta-isomerase | ||||||
Keywords | ISOMERASE | ||||||
Function / homology | Function and homology information steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process Similarity search - Function | ||||||
Biological species | Comamonas testosteroni (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å | ||||||
Authors | Gonzalez, A. / Tsai, Y. / Schwans, J. / Ruben, E. / Sunden, F. / Herschlag, D. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Ketosteroid Isomerase D38NP39GD99N from Pseudomonas Testosteroni (tKSI) with 4-Androstene-3,17-dione Bound Authors: Schwans, J. / Ruben, E. / Sunden, F. / Gonzalez, A. / Tsai, Y. / Herschlag, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nbr.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nbr.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 3nbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nbr_validation.pdf.gz | 1015.1 KB | Display | wwPDB validaton report |
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Full document | 3nbr_full_validation.pdf.gz | 1020 KB | Display | |
Data in XML | 3nbr_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 3nbr_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/3nbr ftp://data.pdbj.org/pub/pdb/validation_reports/nb/3nbr | HTTPS FTP |
-Related structure data
Related structure data | 8choS 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: 13370.069 Da / Num. of mol.: 1 / Mutation: D38NP39GD99N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Comamonas testosteroni (bacteria) / Strain: ATC 11996 / Gene: ksi / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P00947, steroid Delta-isomerase | ||||
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#2: Chemical | #3: Chemical | ChemComp-ASD / | #4: 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: 2.79 Å3/Da / Density % sol: 55.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 2 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.73→52.107 Å / Num. all: 16748 / Num. obs: 16748 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.2 % / Rsym value: 0.058 / Net I/σ(I): 30.9 | |||||||||||||||
Reflection shell | Resolution: 1.73→1.82 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.023 / Mean I/σ(I) obs: 1.4 / Rsym value: 2.265 / % possible all: 99.5 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 8CHO Resolution: 1.73→52.107 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.651 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.128 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→52.107 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 5.0188 Å / Origin y: 46.5499 Å / Origin z: 10.6441 Å
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