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Yorodumi- PDB-1f1b: CRYSTAL STRUCTURE OF E. COLI ASPARTATE TRANSCARBAMOYLASE P268A MU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f1b | |||||||||
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Title | CRYSTAL STRUCTURE OF E. COLI ASPARTATE TRANSCARBAMOYLASE P268A MUTANT IN THE R-STATE IN THE PRESENCE OF N-PHOSPHONACETYL-L-ASPARTATE | |||||||||
Components |
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Keywords | TRANSFERASE / aspartate transcarbamoylase / aspartate carbamoyltransferase / cis-proline / cis-amino acid | |||||||||
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: 2.3 Å | |||||||||
Authors | Jin, L. / Stec, B. / Kantrowitz, E.R. | |||||||||
Citation | Journal: Biochemistry / Year: 2000 Title: A cis-proline to alanine mutant of E. coli aspartate transcarbamoylase: kinetic studies and three-dimensional crystal structures. Authors: Jin, L. / Stec, B. / Kantrowitz, E.R. #1: Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 1999 Title: Insights into the Mechanism of Catalysis and Heterotropic Regulation of Escherichia coli Aspartate Transcarbamoylase based Upon a Structure of the Enzyme Complexed with the Bisubstrate Analog ...Title: Insights into the Mechanism of Catalysis and Heterotropic Regulation of Escherichia coli Aspartate Transcarbamoylase based Upon a Structure of the Enzyme Complexed with the Bisubstrate Analog N-phosphonacetyl-L-aspartate at 2.1 A. 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 | 1f1b.cif.gz | 216.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f1b.ent.gz | 170.6 KB | Display | PDB format |
PDBx/mmJSON format | 1f1b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f1b_validation.pdf.gz | 795.9 KB | Display | wwPDB validaton report |
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Full document | 1f1b_full_validation.pdf.gz | 836.1 KB | Display | |
Data in XML | 1f1b_validation.xml.gz | 51.9 KB | Display | |
Data in CIF | 1f1b_validation.cif.gz | 76 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/1f1b ftp://data.pdbj.org/pub/pdb/validation_reports/f1/1f1b | HTTPS FTP |
-Related structure data
-Links
-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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Details | The biological assembly is a dodecamer. The entire molecule requires two symmetry partners generated by rotations around the three-fold |
-Components
#1: Protein | Mass: 34311.070 Da / Num. of mol.: 2 / Mutation: P268A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Plasmid: PEK412, 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) Plasmid: PEK412, 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: 62.37 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: microdialysis / pH: 5.75 Details: ENZYME: 7.5 mg/ml in 50 uL microdialysis button. BUFFER: 20 mm maleic acid, 3 mM sodium azide, 1 mM N-phosphonacetyl-L-aspartate, pH 5.75, MICRODIALYSIS, temperature 293K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||
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: Jun 9, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 60335 / Num. obs: 58790 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.3→2.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.387 / % possible all: 94 |
-Processing
Software |
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Refinement | Resolution: 2.3→8 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→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: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.196 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
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