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Yorodumi- PDB-6jks: Crystal structure of aspartate transcarbamoylase from Trypanosoma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jks | ||||||
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Title | Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with carbamoyl phosphate (CP) and aspartate (Asp) | ||||||
Components | Aspartate carbamoyltransferase, putative | ||||||
Keywords | TRANSFERASE / ATCase / Pyrimidine metabolism | ||||||
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 | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Matoba, K. / Shiba, T. / Nara, T. / Aoki, T. / Nagasaki, S. / Hayamizu, R. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. ...Matoba, K. / Shiba, T. / Nara, T. / Aoki, T. / Nagasaki, S. / Hayamizu, R. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Balogun, E.O. / Inaoka, D.K. / Kita, K. / Harada, S. | ||||||
Citation | Journal: To Be Published Title: Crystallographic snapshots of Trypanosoma cruzi aspartate transcarbamoylase revealed an ordered Bi-Bi reaction mechanism Authors: Matoba, K. / Shiba, T. / Nara, T. / Aoki, T. / Nagasaki, S. / Hayamizu, R. / Honma, T. / Tanaka, A. / Inoue, M. / Matsuoka, S. / Balogun, E.O. / Inaoka, D.K. / Kita, K. / Harada, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jks.cif.gz | 726.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jks.ent.gz | 607.1 KB | Display | PDB format |
PDBx/mmJSON format | 6jks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jks_validation.pdf.gz | 506.8 KB | Display | wwPDB validaton report |
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Full document | 6jks_full_validation.pdf.gz | 527.7 KB | Display | |
Data in XML | 6jks_validation.xml.gz | 72.5 KB | Display | |
Data in CIF | 6jks_validation.cif.gz | 101.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/6jks ftp://data.pdbj.org/pub/pdb/validation_reports/jk/6jks | HTTPS FTP |
-Related structure data
Related structure data | 6jkqC 6jkrC 6jktC 6jl4C 6jl5C 6jl6C 1ml4S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 36138.820 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (strain CL Brener) (eukaryote) Strain: CL Brener / Gene: Tc00.1047053508375.30 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q4D3W3, aspartate carbamoyltransferase #2: Chemical | ChemComp-CP / #3: Chemical | ChemComp-ASP / #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: 2.46 Å3/Da / Density % sol: 50.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 10% PEG 3350, 0.1 M acetate buffer pH 4.6, 0.2 M ammonium acetate, 0.01 M cobalt chloride and 3% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.3 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 13, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 122210 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.9 / Num. unique obs: 25230 / Rrim(I) all: 0.432 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ML4 Resolution: 2.1→29.44 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.039 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.884 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→29.44 Å
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