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Yorodumi- PDB-6fba: Crystal Structure of truncated aspartate transcarbamoylase from P... -
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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 | ||||||
Components | (Aspartate transcarbamoylase) x 2 | ||||||
Keywords | TRANSFERASE / Falciparum Malaria Pyrimidine biosynthesis Trimer Hit Inhibitor | ||||||
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 / membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Lunev, S. / Bosch, S.S. / Batista, F.A. / Wang, C. / Wrenger, C. / Groves, M.R. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fba.cif.gz | 405.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fba.ent.gz | 333.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fba_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6fba_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6fba_validation.xml.gz | 40.1 KB | Display | |
Data in CIF | 6fba_validation.cif.gz | 54.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/6fba ftp://data.pdbj.org/pub/pdb/validation_reports/fb/6fba | HTTPS FTP |
-Related structure data
Related structure data | 5ilqS 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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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.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: ATCase / Production host: Escherichia coli (E. coli) / References: UniProt: O15804, aspartate carbamoyltransferase #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.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: ATCase / Production host: Escherichia coli (E. coli) / References: UniProt: O15804, aspartate carbamoyltransferase |
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-Non-polymers , 8 types, 158 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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