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Yorodumi- PDB-3mpu: Crystal structure of the C47A/A241C disulfide-linked E. coli Aspa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mpu | ||||||
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Title | Crystal structure of the C47A/A241C disulfide-linked E. coli Aspartate Transcarbamoylase holoenzyme | ||||||
Components |
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Keywords | TRANSFERASE / aspartate trancarbamoylase / disulfide bond / phosphate / catalysis / product release / ordered-sequential mechanism | ||||||
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: 2.855 Å | ||||||
Authors | Mendes, K.R. / Kantrowitz, E.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: The Pathway of Product Release from the R State of Aspartate Transcarbamoylase. Authors: Mendes, K.R. / 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 | 3mpu.cif.gz | 287 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mpu.ent.gz | 232.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mpu_validation.pdf.gz | 491.8 KB | Display | wwPDB validaton report |
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Full document | 3mpu_full_validation.pdf.gz | 530.4 KB | Display | |
Data in XML | 3mpu_validation.xml.gz | 61.6 KB | Display | |
Data in CIF | 3mpu_validation.cif.gz | 86 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/3mpu ftp://data.pdbj.org/pub/pdb/validation_reports/mp/3mpu | HTTPS FTP |
-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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34337.105 Da / Num. of mol.: 3 / Mutation: C47A, A241C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4245, JW4204, pyrB, pyrI / Plasmid: pEK613 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, aspartate carbamoyltransferase #2: Protein | Mass: 17143.625 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: pyrI, b4244, JW4203 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7F3 #3: Chemical | ChemComp-PO4 / #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: 3.14 Å3/Da / Density % sol: 60.87 % |
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Crystal grow | Temperature: 293 K / Method: microdialysis / pH: 5.9 Details: Protein at 10 mg/ml was dialyzed against solution containing 100 mM KH2PO4, 3mM NaN3, pH 5.9, MICRODIALYSIS, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 21, 2009 / Details: fiber-optic taper |
Radiation | Monochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→30 Å / Num. obs: 45620 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 63.2 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 99.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.8 / Num. unique all: 633869 / Rsym value: 0.51 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1D09, chain A Resolution: 2.855→29.923 Å / SU ML: 1.43 / σ(F): 1.33 / Phase error: 24.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.943 Å2 / ksol: 0.251 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.289 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.855→29.923 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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