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Yorodumi- PDB-4zcq: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zcq | ||||||
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Title | Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase in complex with choline | ||||||
Components | Cholinephosphate 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 / nuclear envelope / identical protein binding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 | 4zcq.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zcq.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 4zcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zcq_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 4zcq_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 4zcq_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 4zcq_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/4zcq ftp://data.pdbj.org/pub/pdb/validation_reports/zc/4zcq | HTTPS FTP |
-Related structure data
Related structure data | 4zcpC 4zcrC 4zcsC 4zctSC 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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Unit cell |
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-Components
#1: Protein | Mass: 20810.123 Da / Num. of mol.: 1 / Fragment: UNP residues 581-775 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: isolate 3D7 / Gene: ctP, MAL13P1.86 / Production host: Escherichia coli (E. coli) References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase |
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#2: Chemical | ChemComp-CHT / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 24% PEG 3350, 0.08M NaF |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972957 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972957 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→34.43 Å / Num. obs: 16280 / % possible obs: 99.22 % / Redundancy: 4 % / Rsym value: 0.038 / Net I/σ(I): 15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZCT Resolution: 1.92→34.43 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→34.43 Å
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Refine LS restraints |
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LS refinement shell |
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