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Yorodumi- PDB-2fg7: N-succinyl-L-ornithine transcarbamylase from B. fragilis complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fg7 | ||||||
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Title | N-succinyl-L-ornithine transcarbamylase from B. fragilis complexed with carbamoyl phosphate and N-succinyl-L-norvaline | ||||||
Components | putative ornithine carbamoyltransferase | ||||||
Keywords | TRANSFERASE / alpha/beta | ||||||
Function / homology | Function and homology information N-succinylornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine biosynthetic process via ornithine / citrulline biosynthetic process / amino acid binding Similarity search - Function | ||||||
Biological species | Bacteroides fragilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Shi, D. / Yu, X. / Malamy, M.H. / Allewell, N.M. / Tuchman, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structure and catalytic mechanism of a novel N-succinyl-L-ornithine transcarbamylase in arginine biosynthesis of Bacteroides fragilis. Authors: Shi, D. / Morizono, H. / Cabrera-Luque, J. / Yu, X. / Roth, L. / Malamy, M.H. / Allewell, N.M. / Tuchman, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fg7.cif.gz | 389.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fg7.ent.gz | 319.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fg7_validation.pdf.gz | 534.8 KB | Display | wwPDB validaton report |
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Full document | 2fg7_full_validation.pdf.gz | 584.2 KB | Display | |
Data in XML | 2fg7_validation.xml.gz | 75.3 KB | Display | |
Data in CIF | 2fg7_validation.cif.gz | 100.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/2fg7 ftp://data.pdbj.org/pub/pdb/validation_reports/fg/2fg7 | HTTPS FTP |
-Related structure data
Related structure data | 2fg6SC 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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2 |
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Unit cell |
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Details | The biological unit is a trimer generated by chain X, Y and Z, or C, D and E |
-Components
#1: Protein | Mass: 38630.051 Da / Num. of mol.: 6 / Mutation: T242L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: argF' / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q5LI27, Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases #2: Chemical | #3: Chemical | ChemComp-SN0 / #4: Chemical | ChemComp-CP / #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: 3.18 Å3/Da / Density % sol: 61.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 56% tascimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 2005 |
Radiation | Monochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 64724 / Num. obs: 64660 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 75.5 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6420 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FG6 Resolution: 2.9→19.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1022441.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.7193 Å2 / ksol: 0.318926 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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