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Yorodumi- PDB-3r7f: Crystal Structure of CP-bound Aspartate Transcarbamoylase from Ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r7f | ||||||
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Title | Crystal Structure of CP-bound Aspartate Transcarbamoylase from Bacillus subtilis | ||||||
Components | Aspartate carbamoyltransferase | ||||||
Keywords | TRANSFERASE / Aspartate Transcarbamoylase / Carbamoyl Phosphate / Catalytic Cycle | ||||||
Function / homology | Function and homology information aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å | ||||||
Authors | Cockrell, G.M. / Harris, K.M. / Puleo, D.E. / Kantrowitz, E.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Crystallographic Snapshots of the Complete Catalytic Cycle of the Unregulated Aspartate Transcarbamoylase from Bacillus subtilis. Authors: Harris, K.M. / Cockrell, G.M. / Puleo, D.E. / 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 | 3r7f.cif.gz | 196.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r7f.ent.gz | 157.1 KB | Display | PDB format |
PDBx/mmJSON format | 3r7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/3r7f ftp://data.pdbj.org/pub/pdb/validation_reports/r7/3r7f | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 34266.691 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: pyrB, BSU15490 / Production host: Escherichia coli (E. coli) / References: UniProt: P05654, aspartate carbamoyltransferase #2: Chemical | ChemComp-CP / #3: Chemical | ChemComp-PO4 / #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: 4.77 Å3/Da / Density % sol: 74.24 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 111454 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.085 / Χ2: 1.073 / Net I/σ(I): 11.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→34.117 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8735 / SU ML: 0.19 / σ(F): 1.35 / 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: 43.493 Å2 / ksol: 0.345 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.82 Å2 / Biso mean: 47.8148 Å2 / Biso min: 23.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.101→34.117 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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