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- PDB-6jkr: Crystal structure of aspartate transcarbamoylase from Trypanosoma... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jkr | ||||||
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Title | Crystal structure of aspartate transcarbamoylase from Trypanosoma cruzi in complex with carbamoyl phosphate (CP) | ||||||
![]() | Aspartate carbamoyltransferase | ||||||
![]() | TRANSFERASE / ATCase / Pyrimidine metabolism | ||||||
Function / homology | ![]() aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 765.3 KB | Display | ![]() |
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PDB format | ![]() | 637.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 504.5 KB | Display | ![]() |
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Full document | ![]() | 517.8 KB | Display | |
Data in XML | ![]() | 80.2 KB | Display | |
Data in CIF | ![]() | 117.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jkqSC ![]() 6jksC ![]() 6jktC ![]() 6jl4C ![]() 6jl5C ![]() 6jl6C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CP / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.69 % |
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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: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 277190 / % possible obs: 95.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 25230 / % possible all: 91.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JKQ Resolution: 1.6→29.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.421 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.079 / 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: 18.475 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→29.6 Å
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Refine LS restraints |
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