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Yorodumi- PDB-3d7s: Crystal structure of Wild-Type E. Coli Asparate Transcarbamoylase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d7s | ||||||
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Title | Crystal structure of Wild-Type E. Coli Asparate Transcarbamoylase at pH 8.5 at 2.80 A Resolution | ||||||
Components |
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Keywords | TRANSFERASE / high ph / positively charged channel / apoenzyme / Pyrimidine biosynthesis / Metal-binding / Zinc | ||||||
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: 2.8 Å | ||||||
Authors | Stieglitz, K.A. / Xia, J. / Kantrowitz, E.R. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: The first high pH structure of Escherichia coli aspartate transcarbamoylase. Authors: Stieglitz, K.A. / Xia, J. / 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 | 3d7s.cif.gz | 192.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d7s.ent.gz | 152.9 KB | Display | PDB format |
PDBx/mmJSON format | 3d7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d7s_validation.pdf.gz | 462.2 KB | Display | wwPDB validaton report |
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Full document | 3d7s_full_validation.pdf.gz | 560.8 KB | Display | |
Data in XML | 3d7s_validation.xml.gz | 48.5 KB | Display | |
Data in CIF | 3d7s_validation.cif.gz | 66 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/3d7s ftp://data.pdbj.org/pub/pdb/validation_reports/d7/3d7s | HTTPS FTP |
-Related structure data
Related structure data | 1skuS 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: 34337.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pyrB, b4245, JW4204 / 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) / Strain: K12 / Gene: pyrI, b4244, JW4203 / Plasmid: PEK54 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3, aspartate carbamoyltransferase #3: Chemical | #4: 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: 3.12 Å3/Da / Density % sol: 60.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 50 mM Tris 8K PEG, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 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 31, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 33566 / Num. obs: 30682 / % possible obs: 90.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.8→2.8 Å / Redundancy: 3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2200 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SKU Resolution: 2.8→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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