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Yorodumi- PDB-4ekn: Structure of the catalytic chain of Methanococcus jannaschii Aspa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ekn | ||||||
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Title | Structure of the catalytic chain of Methanococcus jannaschii Aspartate Transcarbamoylase in a hexagonal crystal form | ||||||
Components | Aspartate carbamoyltransferase | ||||||
Keywords | TRANSFERASE / ATCase / aspartate transcarbamoylase / pyrimidine biosynthesis / thermostability / substrate channeling | ||||||
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: 2.4996 Å | ||||||
Authors | Vitali, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Structure of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase in a hexagonal crystal form: insights into the path of carbamoyl phosphate to the active site of the enzyme. Authors: Vitali, J. / Singh, A.K. / Soares, A.S. / Colaneri, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ekn.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ekn.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ekn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ekn_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 4ekn_full_validation.pdf.gz | 454.3 KB | Display | |
Data in XML | 4ekn_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 4ekn_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/4ekn ftp://data.pdbj.org/pub/pdb/validation_reports/ek/4ekn | HTTPS FTP |
-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 on special symmetry positions |
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Details | Trimer. A hexamer is also formed by pisa prediction but it is not known if it has biological relevance |
-Components
#1: Protein | Mass: 35210.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Description: pSJS1240 was also cotransformed / Gene: MJ1581, pyrB / Plasmid: pEK406 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1594 / References: UniProt: Q58976, aspartate carbamoyltransferase | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.21 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.0 M ammonium sulfate, 0.2 M potassium sodium tartrate tetrahydrate, and 0.1 M Tris-HCl pH 7.5. The protein was a mixture of catalytic and regulatory subunits at a molar ratio of 1:1 ...Details: 2.0 M ammonium sulfate, 0.2 M potassium sodium tartrate tetrahydrate, and 0.1 M Tris-HCl pH 7.5. The protein was a mixture of catalytic and regulatory subunits at a molar ratio of 1:1 concentrated to 11 mg/ml. Drops consisted of 2ul reservoir and 2.6 ul complex solution., VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 18, 2010 |
Radiation | Monochromator: Si(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4996→50 Å / Num. obs: 13471 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.4996→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.62 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY of 2RGW chain D Resolution: 2.4996→41.985 Å / SU ML: 0.35 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Phase error: 24.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.097 Å2 / ksol: 0.405 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4996→41.985 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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