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Yorodumi- PDB-4zcs: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zcs | ||||||
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Title | Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase in complex with CDP-choline | ||||||
Components | Choline-phosphate cytidylyltransferase | ||||||
Keywords | TRANSFERASE / enzyme / malaria / cytidylyltransferase / phosphatidylcholine | ||||||
Function / homology | Function and homology information Synthesis of PC / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / phosphatidylcholine binding / identical protein binding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Guca, E. / Hoh, F. / Guichou, J.-F. / Cerdan, R. | ||||||
Funding support | France, 1items
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Citation | Journal: Sci Rep / Year: 2018 Title: Structural determinants of the catalytic mechanism of Plasmodium CCT, a key enzyme of malaria lipid biosynthesis. Authors: Guca, E. / Nagy, G.N. / Hajdu, F. / Marton, L. / Izrael, R. / Hoh, F. / Yang, Y. / Vial, H. / Vertessy, B.G. / Guichou, J.F. / Cerdan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zcs.cif.gz | 197 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zcs.ent.gz | 156.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zcs_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 4zcs_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 4zcs_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 4zcs_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/4zcs ftp://data.pdbj.org/pub/pdb/validation_reports/zc/4zcs | HTTPS FTP |
-Related structure data
Related structure data | 4zcpC 4zcqC 4zcrC 4zctC 3hl4S C: citing same article (ref.) 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
#1: Protein | Mass: 20810.123 Da / Num. of mol.: 6 / Fragment: UNP residues 581-775 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Gene: PF3D7_1316600 / Production host: Escherichia coli (E. coli) References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase #2: Chemical | ChemComp-CDC / [ #3: Chemical | #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: 3.01 Å3/Da / Density % sol: 59.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.2M NaF, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979338 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979338 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→113.67 Å / Num. obs: 52521 / % possible obs: 99.63 % / Redundancy: 9.35 % / Rsym value: 0.32 / Net I/σ(I): 0.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HL4 Resolution: 2.45→113.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.35 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.051 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→113.67 Å
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Refine LS restraints |
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