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Yorodumi- PDB-1d09: ASPARTATE TRANSCARBAMOYLASE COMPLEXED WITH N-PHOSPHONACETYL-L-ASP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d09 | |||||||||
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Title | ASPARTATE TRANSCARBAMOYLASE COMPLEXED WITH N-PHOSPHONACETYL-L-ASPARTATE (PALA) | |||||||||
Components |
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Keywords | TRANSFERASE / PROTEIN-INHIBITOR COMPLEX ASPARTATE TRANSCARBAMOYLASE ASPARTATE TRANSCARBAMYLASE | |||||||||
Function / homology | Function and homology information aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | |||||||||
Authors | Jin, L. / Stec, B. / Lipscomb, W.N. / Kantrowitz, E.R. | |||||||||
Citation | Journal: Proteins / Year: 1999 Title: Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate ...Title: Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate at 2.1 A. Authors: Jin, L. / Stec, B. / Lipscomb, W.N. / Kantrowitz, E.R. #1: Journal: J.Mol.Biol. / Year: 1988 Title: Complex of N-phosphonacetyl-L-aspartate with Aspartate carbamoyltransferase Authors: Ke, H. / Lipscomb, W.N. / Cho, Y. / Honzatko, R.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d09.cif.gz | 203.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d09.ent.gz | 163.4 KB | Display | PDB format |
PDBx/mmJSON format | 1d09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d09_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1d09_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1d09_validation.xml.gz | 45.6 KB | Display | |
Data in CIF | 1d09_validation.cif.gz | 65.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/1d09 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/1d09 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34337.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH N-PHOSPHONACETYL-L-ASPARTATE / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NATURAL PYRB PROMOTOR Plasmid: PEK54, A PLASMID WITH THE PYRBI GENES INSERTED INTO PUC119 Production host: Escherichia coli (E. coli) / References: UniProt: P0A786, aspartate carbamoyltransferase #2: Protein | Mass: 17143.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRI Plasmid: PEK54, A PLASMID WITH THE PYRBI GENES INSERTED INTO PUC119 Production host: Escherichia coli (E. coli) / References: UniProt: P0A7F3 #3: Chemical | #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: 3.27 Å3/Da / Density % sol: 62.43 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: liquid diffusion / pH: 5.9 Details: ENZYME: 12 MG/ML; BUFFER: 50 MM MALEIC ACID, 3 MM SOLDIUM AZIDE 1 MM N- PHOSPHONACETYL-L-ASPARTATE, pH 5.9, LIQUID DIFFUSION | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / Method: microdialysis / Details: Krause, K.L., (1987) J.Mol.Biol., 193, 527. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: UCSD MARK III / Detector: AREA DETECTOR / Date: Dec 5, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→8 Å / Num. all: 74685 / Num. obs: 73113 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.437 / % possible all: 90.7 |
Reflection | *PLUS Num. obs: 74685 / % possible obs: 94 % / Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Resolution: 2.1→8 Å / σ(F): 2 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 8 Å / Num. reflection obs: 73113 / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / Rfactor Rfree: 0.364 / Rfactor Rwork: 0.34 |