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Yorodumi- PDB-4xsv: Human CTP: Phosphoethanolamine Cytidylyltransferase in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xsv | ||||||
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Title | Human CTP: Phosphoethanolamine Cytidylyltransferase in complex with CTP | ||||||
Components | Ethanolamine-phosphate cytidylyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information ethanolamine-phosphate cytidylyltransferase / ethanolamine-phosphate cytidylyltransferase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / phospholipid biosynthetic process / endoplasmic reticulum membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Schuler, H. / Karlberg, T. | ||||||
Citation | Journal: To Be Published Title: Human CTP: Phosphoethanolamine Cytidylyltransferase Authors: Schuler, H. / Karlberg, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xsv.cif.gz | 135.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xsv.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 4xsv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/4xsv ftp://data.pdbj.org/pub/pdb/validation_reports/xs/4xsv | HTTPS FTP |
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-Related structure data
Related structure data | 3elbS 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: 38789.859 Da / Num. of mol.: 1 / Fragment: UNP residues 18-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PCYT2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 pRARE References: UniProt: Q99447, ethanolamine-phosphate cytidylyltransferase |
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#2: Chemical | ChemComp-C5P / |
#3: Chemical | ChemComp-CTP / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 17% PEG3350, 0.2M magnesium formate, 0.1M HEPES, 0.01M CTP, 0.01M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9333 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9333 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 11119 / Num. obs: 11119 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rmerge(I) obs: 0.131 / Rsym value: 0.129 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 4.6 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ELB Resolution: 2.7→39.37 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.874 / SU B: 25.232 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.273 / ESU R Free: 0.356 / 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: 34.017 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→39.37 Å
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Refine LS restraints |
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