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Yorodumi- PDB-2a0f: Structure of D236A mutant E. coli Aspartate Transcarbamoylase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a0f | ||||||
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Title | Structure of D236A mutant E. coli Aspartate Transcarbamoylase in presence of Phosphonoacetamide at 2.90 A resolution | ||||||
Components |
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Keywords | transferase/transferase regulator / homotropic cooperativity / catalytic cycle / allosteric regulation / Alternate conformations / transferase-transferase regulator COMPLEX | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Stieglitz, K.A. / Dusinberre, K.J. / Cardia, J.P. / Tsuruta, H. / Kantrowitz, E.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structure of the E.coli Aspartate Transcarbamoylase Trapped in the Middle of the Catalytic Cycle. Authors: Stieglitz, K.A. / Dusinberre, K.J. / Cardia, J.P. / Tsuruta, H. / 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 | 2a0f.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a0f.ent.gz | 154.1 KB | Display | PDB format |
PDBx/mmJSON format | 2a0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a0f_validation.pdf.gz | 482.9 KB | Display | wwPDB validaton report |
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Full document | 2a0f_full_validation.pdf.gz | 614.7 KB | Display | |
Data in XML | 2a0f_validation.xml.gz | 57.6 KB | Display | |
Data in CIF | 2a0f_validation.cif.gz | 80 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/2a0f ftp://data.pdbj.org/pub/pdb/validation_reports/a0/2a0f | HTTPS FTP |
-Related structure data
Related structure data | 8at1S 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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Unit cell |
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-Components
#1: Protein | Mass: 34293.098 Da / Num. of mol.: 2 / Mutation: D236A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrB / Plasmid: pEK152 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / 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: pEK114 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3 #3: Chemical | ChemComp-PCT / | #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: 3.7 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 5.7 Details: maleic acid, sodium azide, phosphonoacetamide, pH 5.7, MICRODIALYSIS, temperature 298K |
-Data collection
Diffraction | Mean temperature: 97 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 16, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 29423 / Num. obs: 26586 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.36 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4 % / Rmerge(I) obs: 0.4 / Num. unique all: 2900 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 8AT1 Resolution: 2.9→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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