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- PDB-7pui: Crystal structure of the C-terminal catalytic domain of Plasmodiu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pui | |||||||||
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Title | Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum CTP:phosphocholine cytidylyltransferase with 2-pyridineboronic acid | |||||||||
![]() | Cholinephosphate cytidylyltransferase | |||||||||
![]() | TRANSFERASE / Plasmodium Falciparum CCT Inhibitors Fragments | |||||||||
Function / homology | ![]() Synthesis of PC / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / phosphatidylcholine binding / nuclear envelope / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Duclovel, C. / Gelin, M. / Krimm, I. / Cerdan, R. / Guichou, J.-F. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.4 KB | Display | ![]() |
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PDB format | ![]() | 51.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 689 KB | Display | ![]() |
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Full document | ![]() | 689.1 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q2kC ![]() 7q2mC ![]() 7q3mC ![]() 7q3wC ![]() 7q9wC ![]() 7qadC ![]() 7z9vC ![]() 4zctS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ctP, MAL13P1.86 / Production host: ![]() ![]() References: UniProt: Q8IEE9, choline-phosphate cytidylyltransferase |
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#2: Chemical | ChemComp-86Z / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.09 % |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
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: 2.08→59.59 Å / Num. obs: 12538 / % possible obs: 98.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 47.76 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.046 / Rrim(I) all: 0.1 / Net I/σ(I): 8.7 / Num. measured all: 56095 / Scaling rejects: 8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZCT Resolution: 2.08→59.59 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.16 / 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: 103.76 Å2 / Biso mean: 59.5582 Å2 / Biso min: 37.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.08→59.59 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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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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