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Yorodumi- PDB-3hdj: The crystal structure of probable ornithine cyclodeaminase from B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hdj | ||||||
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Title | The crystal structure of probable ornithine cyclodeaminase from Bordetella pertussis Tohama I | ||||||
Components | Probable ornithine cyclodeaminase | ||||||
Keywords | structural genomics / unknown function / APC62486 / ornithine cyclodeaminase / Bordetella pertussis Tohama I / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG | ||||||
Function / homology | Function and homology information ornithine cyclodeaminase, domain 1 / ornithine cyclodeaminase, domain 1 / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bordetella pertussis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Tan, K. / Sather, A. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of probable ornithine cyclodeaminase from Bordetella pertussis Tohama I Authors: Tan, K. / Sather, A. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hdj.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hdj.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/3hdj ftp://data.pdbj.org/pub/pdb/validation_reports/hd/3hdj | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Experimentally unknown. The chains A and B are predicted to form a dimer. |
-Components
#1: Protein | Mass: 32796.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / Strain: Tohama I / Gene: Bordetella pertussis, BP0354 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q7VSP8 #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #5: 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: 2.59 Å3/Da / Density % sol: 52.42 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.5M NaCl, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2008 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→39.5 Å / Num. all: 73662 / Num. obs: 73662 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.64 / Num. unique all: 3592 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→39.41 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.82 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.101 / ESU R Free: 0.101 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.378 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→39.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 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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