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Yorodumi- PDB-4ep1: Crystal structure of anabolic ornithine carbamoyltransferase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ep1 | ||||||
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Title | Crystal structure of anabolic ornithine carbamoyltransferase from Bacillus anthracis | ||||||
Components | Ornithine carbamoyltransferaseOrnithine transcarbamylase | ||||||
Keywords | TRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / trimer / ornithine carbamoyltransferase | ||||||
Function / homology | Function and homology information ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine biosynthetic process / amino acid binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Shabalin, I.G. / Mikolajczak, K. / Stam, J. / Winsor, J. / Shuvalova, L. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal structures of anabolic ornithine carbamoyltransferase from Bacillus anthracis Authors: Shabalin, I.G. / Mikolajczak, K. / Stam, J. / Winsor, J. / Shuvalova, L. / Anderson, W.F. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ep1.cif.gz | 243.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ep1.ent.gz | 198.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ep1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/4ep1 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/4ep1 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 4 - 312 / Label seq-ID: 28 - 336
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-Components
#1: Protein | Mass: 38120.352 Da / Num. of mol.: 2 / Mutation: K191R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: argF, BAS4036, BA_4351, GBAA_4351 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81M99, ornithine carbamoyltransferase |
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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: 3.32 Å3/Da / Density % sol: 62.94 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: Protein: 10 mg/ml in 10 mM Tris-HCl pH 8.3, 500 mM NaCl and 5 mM b-mercaptoethanol. Precipitant: 0.2M potassium sodium tartrate, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-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 315r / Detector: CCD / Date: Mar 3, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→50 Å / Num. obs: 16913 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 87.7 Å2 / Rmerge(I) obs: 0.163 / Rsym value: 0.163 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 3.25→3.31 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 3.1 / Num. unique all: 793 / Rsym value: 0.931 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SwissModel-generated model Resolution: 3.25→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 1 / SU B: 36.408 / SU ML: 0.263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES: WITH TLS ADDED. 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 max: 186.26 Å2 / Biso mean: 84.0478 Å2 / Biso min: 48.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 10485 / Refine-ID: X-RAY DIFFRACTION / Rms: 0.07 / Type: LOCAL / Weight: 0.05
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LS refinement shell | Resolution: 3.25→3.334 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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