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Yorodumi- PDB-7q9v: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q9v | ||||||
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Title | Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 1-(1,3-oxazol-4-yl)methanamine | ||||||
Components | Cholinephosphate cytidylyltransferase | ||||||
Keywords | TRANSFERASE / Plasmodium Falciparum CCT Inhibitors Fragments | ||||||
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: 1.5 Å | ||||||
Authors | Duclovel, C. / Gelin, M. / Krimm, I. / Cerdan, R. / Guichou, J.-F. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design of PfCCT inhibitors Authors: Duclovel, C. / Gelin, M. / Wein, S. / Wengelnik, K. / Krimm, I. / 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 | 7q9v.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q9v.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 7q9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7q9v_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7q9v_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7q9v_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 7q9v_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/7q9v ftp://data.pdbj.org/pub/pdb/validation_reports/q9/7q9v | HTTPS FTP |
-Related structure data
Related structure data | 7pveC 7pvfC 7pvgC 7py9C 7pyaC 7pybC 7pycC 7q2iC 7q2lC 7q2vC 7qa7C 7qd3C 7qvnC 7qvoC 4zctS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20810.123 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: ctP, MAL13P1.86 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase | ||||||
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#2: Chemical | ChemComp-GZ6 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.73 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion / pH: 8 Details: PEG 4000 19%, TRIS pH8 0.1M 6-7-8-9-10% Guanidine HCl 5-6-7% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 12, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96546 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.31→40.8 Å / Num. obs: 32949 / % possible obs: 96.1 % / Redundancy: 2.15 % / Biso Wilson estimate: 20.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05205 / Rrim(I) all: 0.068 / Χ2: 0.832 / Net I/σ(I): 8.3 / Num. measured all: 196430 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZCT Resolution: 1.5→40.8 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 24.96 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.71 Å2 / Biso mean: 26.8471 Å2 / Biso min: 15.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→40.8 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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