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Yorodumi- PDB-3kzn: Crystal structure of N-acetyl-L-ornithine transcarbamylase comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kzn | |||||||||
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Title | Crystal structure of N-acetyl-L-ornithine transcarbamylase complexed with N-acetyl-L-ornirthine | |||||||||
Components | N-acetylornithine carbamoyltransferase | |||||||||
Keywords | TRANSFERASE / transcarbamylase / Amino-acid biosynthesis / Arginine biosynthesis / Cytoplasm | |||||||||
Function / homology | Function and homology information N-acetylornithine carbamoyltransferase / N-acetylornithine carbamoyltransferase activity / ornithine carbamoyltransferase activity / citrulline biosynthetic process / arginine biosynthetic process via ornithine / amino acid binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Shi, D. / Yu, X. / Allewell, N.M. / Tuchman, M. | |||||||||
Citation | Journal: Proteins / Year: 2006 Title: Structures of N-acetylornithine transcarbamoylase from Xanthomonas campestris complexed with substrates and substrate analogs imply mechanisms for substrate binding and catalysis. Authors: Shi, D. / Yu, X. / Roth, L. / Morizono, H. / Tuchman, M. / Allewell, N.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kzn.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kzn.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 3kzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kzn_validation.pdf.gz | 466.1 KB | Display | wwPDB validaton report |
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Full document | 3kzn_full_validation.pdf.gz | 468.4 KB | Display | |
Data in XML | 3kzn_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 3kzn_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/3kzn ftp://data.pdbj.org/pub/pdb/validation_reports/kz/3kzn | HTTPS FTP |
-Related structure data
Related structure data | 3kzmC 3kzoC 3kzkS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40133.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria) Strain: ATCC 33913 / Gene: argF, argF', XCC2249 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8P8J2, N-acetylornithine carbamoyltransferase | ||||
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#2: Chemical | ChemComp-AOR / | ||||
#3: Chemical | #4: Chemical | #5: 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: 2.29 Å3/Da / Density % sol: 46.32 % |
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Crystal grow | Temperature: 291 K / Method: hanging drop / pH: 6 Details: Lithium sulfate, Bis-tris, PEG3350, pH 6.0, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2004 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9186 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 34091 / Num. obs: 33955 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.8 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3KZK Resolution: 1.8→41.17 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.33 / Data cutoff high absF: 4237428 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.121 Å2 / ksol: 0.387 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.09 Å2 / Biso mean: 28.648 Å2 / Biso min: 9.61 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→41.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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