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Yorodumi- PDB-1ml4: The PALA-liganded Aspartate transcarbamoylase catalytic subunit f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ml4 | ||||||
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Title | The PALA-liganded Aspartate transcarbamoylase catalytic subunit from Pyrococcus abyssi | ||||||
Components | Aspartate TranscarbamoylaseAspartate carbamoyltransferase | ||||||
Keywords | TRANSFERASE / BETA PLEATED SHEET / PROTEIN INHIBITOR COMPLEX | ||||||
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 | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Van Boxstael, S. / Cunin, R. / Maes, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Aspartate Transcarbamylase from the Hyperthermophilic Archaeon Pyrococcus abyssi: Thermostability and 1.8A Resolution Crystal Structure of the Catalytic Subunit Complexed With the Bisubstrate ...Title: Aspartate Transcarbamylase from the Hyperthermophilic Archaeon Pyrococcus abyssi: Thermostability and 1.8A Resolution Crystal Structure of the Catalytic Subunit Complexed With the Bisubstrate Analogue N-Phosphonacetyl-L-aspartate. Authors: Van Boxstael, S. / Cunin, R. / Khan, S. / Maes, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ml4.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ml4.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ml4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/1ml4 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/1ml4 | HTTPS FTP |
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-Related structure data
Related structure data | 1ekxS 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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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a trimer generated by the operations : -Y,X-Y,Z and -X+Y,-X,Z |
-Components
#1: Protein | Mass: 34954.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: PyrB / Plasmid: Ptrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): C600ATC- / References: UniProt: P77918, aspartate carbamoyltransferase |
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#2: Chemical | ChemComp-PAL / |
#3: 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: 2.52 Å3/Da / Density % sol: 50.87 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: citric acid, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 8.2 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 24, 2001 |
Radiation | Monochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 29667 / Num. obs: 29667 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.38 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 10.69 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.91 / Num. unique all: 2958 / Rsym value: 0.33 / % possible all: 93 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 70669 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / % possible obs: 93 % / Mean I/σ(I) obs: 3.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb 1EKX Resolution: 1.8→25 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: Rfree / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS VERSION FOR HEMIHEDRAL TWINNED DATA
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Displacement parameters | Biso mean: 27.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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LS refinement shell |
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Xplor file |
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Refinement | *PLUS Lowest resolution: 25 Å / Rfactor Rfree: 0.2118 / Rfactor Rwork: 0.1718 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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