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Yorodumi- PDB-2air: T-state Active Site of Aspartate Transcarbamylase:Crystal Structu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2air | ||||||
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Title | T-state Active Site of Aspartate Transcarbamylase:Crystal Structure of the Carbamyl Phosphate and L-alanosine Ligated Enzyme | ||||||
Components | (Aspartate carbamoyltransferase ...) x 2 | ||||||
Keywords | TRANSFERASE / Aspartate Transcarbamylase / Alanosine / Carbamyl Phosphate / T-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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Huang, J. / Lipscomb, W.N. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: T-State Active Site of Aspartate Transcarbamylase: Crystal Structure of the Carbamyl Phosphate and l-Alanosine Ligated Enzyme Authors: Huang, J. / Lipscomb, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2air.cif.gz | 207.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2air.ent.gz | 164.4 KB | Display | PDB format |
PDBx/mmJSON format | 2air.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/2air ftp://data.pdbj.org/pub/pdb/validation_reports/ai/2air | HTTPS FTP |
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-Related structure data
Related structure data | 1d09S 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 on special symmetry positions |
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-Components
-Aspartate carbamoyltransferase ... , 2 types, 4 molecules AGBH
#1: Protein | Mass: 34337.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrB / 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.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrI / Plasmid: pEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3 |
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-Non-polymers , 4 types, 612 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 3.09 Å3/Da / Density % sol: 60.15 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG-4000, iso-propranol, sodium azide, pH 7.5, 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: 0.9186 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 9, 2004 / Details: mirrors |
Radiation | Monochromator: Horizontally bent si (111), assymetrically cut with water cooled Cu block Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9186 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 130959 / Num. obs: 74502 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 0.71 / Num. unique all: 2377 / % possible all: 56.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D09 Resolution: 2→30 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: 57.36 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å
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