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Yorodumi- PDB-1q95: Aspartate Transcarbamylase (ATCase) of Escherichia coli: A New Cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q95 | ||||||
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Title | Aspartate Transcarbamylase (ATCase) of Escherichia coli: A New Crystalline R State Bound to PALA, or to Product Analogues Phosphate and Citrate | ||||||
Components |
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Keywords | TRANSFERASE / Aspartate Transcarbamylase / Aspartate Carbamoyltransferase / N-carbamyl-L-aspartate / PALA / ATCase-PALA Complex / R state | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Huang, J. / Lipscomb, W.N. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Aspartate Transcarbamylase (ATCase) of Escherichia coli: A New Crystalline R-State Bound to PALA, or to Product Analogues Citrate and Phosphate Authors: Huang, J. / Lipscomb, W.N. #1: 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 2.1A Authors: Jin, L. / Stec, B. / Lipscomb, W.N. / Kantrowitz, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q95.cif.gz | 552 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q95.ent.gz | 454.1 KB | Display | PDB format |
PDBx/mmJSON format | 1q95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q95_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 1q95_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 1q95_validation.xml.gz | 122 KB | Display | |
Data in CIF | 1q95_validation.cif.gz | 160.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/1q95 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/1q95 | HTTPS FTP |
-Related structure data
Related structure data | 1r0bC 1d09S 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
#1: Protein | Mass: 34337.105 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: PYRB OR B4245 OR C5345 OR Z5856 OR ECS5222 OR SF4245 OR S4507 Plasmid: pEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase #2: Protein | Mass: 17143.625 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRI OR B4244 OR C5344 OR Z5855 OR ECS5221 / Plasmid: pEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3 #3: Chemical | ChemComp-PAL / #4: Chemical | ChemComp-ZN / #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: 2.89 Å3/Da / Density % sol: 57.51 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG-mmes 2000, lithium sulfate, sodium azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.928 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 22, 2001 / Details: mirrors |
Radiation | Monochromator: Horizontally bent si(111), assymetrically cut with water coooled Cu block Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→50 Å / Num. all: 147443 / Num. obs: 113497 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.5 / Redundancy: 1.3 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 0.074 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.46→2.55 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 9571 / Rsym value: 0.41 / % possible all: 74.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D09 Resolution: 2.46→8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 63.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.46→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.46→2.55 Å
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