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- PDB-3l05: Crystal structure of N-acetyl-L-ornithine transcarbamylase E92S m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3l05 | |||||||||
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Title | Crystal structure of N-acetyl-L-ornithine transcarbamylase E92S mutant complexed with carbamyl phosphate and N-succinyl-L-norvaline | |||||||||
![]() | N-acetylornithine carbamoyltransferase | |||||||||
![]() | TRANSFERASE / Transcarbamylase / Amino-acid biosynthesis / Arginine biosynthesis | |||||||||
Function / homology | ![]() N-acetylornithine carbamoyltransferase / N-acetylornithine carbamoyltransferase activity / ornithine carbamoyltransferase activity / arginine biosynthetic process via ornithine / citrulline biosynthetic process / amino acid binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Shi, D. / Yu, X. / Allewell, N.M. / Tuchman, M. | |||||||||
![]() | ![]() Title: A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase. Authors: Shi, D. / Yu, X. / Cabrera-Luque, J. / Chen, T.Y. / Roth, L. / Morizono, H. / Allewell, N.M. / Tuchman, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.2 KB | Display | ![]() |
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PDB format | ![]() | 61 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.8 KB | Display | ![]() |
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Full document | ![]() | 471.8 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2g7mC ![]() 3l02C ![]() 3l04C ![]() 3l06C ![]() 3kzoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 40091.531 Da / Num. of mol.: 1 / Mutation: E92S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 33913 / Gene: argF, argF', XCC2249 / Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: Q8P8J2, N-acetylornithine carbamoyltransferase |
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#2: Chemical | ChemComp-SN0 / |
#3: Chemical | ChemComp-CP / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Lithium sulfate, Bis-tris, PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 27, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 8953 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 110.9 Å2 / Rmerge(I) obs: 0.153 / Χ2: 1.028 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 3.3 / Num. unique all: 875 / Χ2: 1.063 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3KZO Resolution: 2.8→30.4 Å / Rfactor Rfree error: 0.012 / Occupancy max: 1 / Occupancy min: 0.33 / Data cutoff high absF: 2163796 / 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: 29.582 Å2 / ksol: 0.328 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.96 Å2 / Biso mean: 38.489 Å2 / Biso min: 11.52 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→30.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
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Xplor file |
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