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Yorodumi- PDB-3e2p: Catalytic subunit of M. Jannaschii aspartate transcarbamoylase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e2p | ||||||
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Title | Catalytic subunit of M. Jannaschii aspartate transcarbamoylase in an orthorhombic crystal form | ||||||
Components | Aspartate carbamoyltransferase | ||||||
Keywords | TRANSFERASE / Aspartate Transcarbamoylase / ATCase / pyrimidine biosynthesis / thermostability / Methanococcus jannaschii | ||||||
Function / homology | Function and homology information aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Vitali, J. / Colaneri, M.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase in an orthorhombic crystal form. Authors: Vitali, J. / Colaneri, M.J. #1: Journal: PROTEINS / Year: 2008 Title: Crystal structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylas Authors: Vitali, J. / Colaneri, M.J. / Kantrowitz, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e2p.cif.gz | 652.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e2p.ent.gz | 558.6 KB | Display | PDB format |
PDBx/mmJSON format | 3e2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/3e2p ftp://data.pdbj.org/pub/pdb/validation_reports/e2/3e2p | HTTPS FTP |
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-Related structure data
Related structure data | 2rgwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35210.621 Da / Num. of mol.: 12 / Fragment: catalytic subunit Source method: isolated from a genetically manipulated source Details: PSJS1240 was also co-transformed Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: pyrB, MJ1581 / Plasmid: pEK406 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1594 / References: UniProt: Q58976, aspartate carbamoyltransferase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.5 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: SI (111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. obs: 92280 / % possible obs: 99.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 73.3 Å2 / Rmerge(I) obs: 0.095 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.4 / Num. unique all: 8844 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RGW Resolution: 3→40 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: 70 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→40 Å
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Refine LS restraints |
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