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Yorodumi- PDB-2g7m: Crystal structure of B. fragilis N-succinylornithine transcarbamy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g7m | ||||||
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Title | Crystal structure of B. fragilis N-succinylornithine transcarbamylase P90E mutant complexed with carbamoyl phosphate and N-acetylnorvaline | ||||||
Components | putative ornithine carbamoyltransferaseOrnithine transcarbamylase | ||||||
Keywords | TRANSFERASE / Alpha/beta | ||||||
Function / homology | Function and homology information N-succinylornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine 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. / Roth, L. / Morizono, H. / Allewell, N.M. / Tuchman, M. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g7m.cif.gz | 386.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g7m.ent.gz | 317.7 KB | Display | PDB format |
PDBx/mmJSON format | 2g7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/2g7m ftp://data.pdbj.org/pub/pdb/validation_reports/g7/2g7m | HTTPS FTP |
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-Related structure data
Related structure data | 3l02C 3l04C 3l05C 3l06C 2fg7S C: citing same article (ref.) S: Starting model for refinement |
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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: 38662.047 Da / Num. of mol.: 6 / Mutation: P90E, T242L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: argF' / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: GenBank: 60491451, UniProt: Q64Z33*PLUS, Transferases; Transferring one-carbon groups; Carboxy- and carbamoyltransferases #2: Chemical | ChemComp-AN0 / #3: Chemical | ChemComp-CP / #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: 3.18 Å3/Da / Density % sol: 61.29 % |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 5.5 Details: 1.5M ammonium sulfate, 100mM Bis-tris, pH 5.5, EVAPORATION, 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: Feb 14, 2006 / Details: mirror |
Radiation | Monochromator: mirror / 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→30 Å / Num. all: 64435 / Num. obs: 64177 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6363 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2FG7 Resolution: 2.9→19.78 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 825751.5 / 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: 35.658 Å2 / ksol: 0.325694 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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