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- PDB-6fba: Crystal Structure of truncated aspartate transcarbamoylase from P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fba | ||||||
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Title | Crystal Structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with bound inhibitor 2,3-naphthalenediol | ||||||
![]() | (Aspartate transcarbamoylase) x 2 | ||||||
![]() | TRANSFERASE / Falciparum Malaria Pyrimidine biosynthesis Trimer Hit Inhibitor | ||||||
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 / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lunev, S. / Bosch, S.S. / Batista, F.A. / Wang, C. / Wrenger, C. / Groves, M.R. | ||||||
![]() | ![]() Title: Identification of a non-competitive inhibitor of Plasmodium falciparum aspartate transcarbamoylase. Authors: Lunev, S. / Bosch, S.S. / Batista, F.A. / Wang, C. / Li, J. / Linzke, M. / Kruithof, P. / Chamoun, G. / Domling, A.S.S. / Wrenger, C. / Groves, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 405.5 KB | Display | ![]() |
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PDB format | ![]() | 333.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 54.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ilqS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 40350.762 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ATCase / Production host: ![]() ![]() #2: Protein | | Mass: 40366.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: CYS 212 was modelled as CSO Source: (gene. exp.) ![]() ![]() Gene: ATCase / Production host: ![]() ![]() |
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-Non-polymers , 8 types, 158 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/D48.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/D48.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-NA / | #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.49 % / Description: Trimer |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Bis-tris propane pH 7.5 200 mM Na-sulphate 15 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→75.14 Å / Num. all: 228939 / Num. obs: 74373 / % possible obs: 98.7 % / Observed criterion σ(I): 1.45 / Redundancy: 3.16 % / CC1/2: 0.998 / Rrim(I) all: 0.081 / Net I/σ(I): 11.46 |
Reflection shell | Resolution: 2.05→2.17 Å / Redundancy: 3.185 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 11695 / CC1/2: 0.506 / Rrim(I) all: 0.988 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ILQ Resolution: 2→75.13 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.505 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.151 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.799 Å2
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Refinement step | Cycle: 1 / Resolution: 2→75.13 Å
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Refine LS restraints |
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