[English] 日本語
Yorodumi- PDB-3elb: Human CTP: Phosphoethanolamine Cytidylyltransferase in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3elb | ||||||
---|---|---|---|---|---|---|---|
Title | Human CTP: Phosphoethanolamine Cytidylyltransferase in complex with CMP | ||||||
Components | Ethanolamine-phosphate cytidylyltransferase | ||||||
Keywords | TRANSFERASE / Kennedy pathway / CMP / CTP / Phosphoethanolamine / cytidylyltransferase / SGC / Structural Genomics Consortium / Nucleotidyltransferase / Phospholipid biosynthesis | ||||||
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 / SAD / Resolution: 2 Å | ||||||
Authors | Karlberg, T. / Welin, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. ...Karlberg, T. / Welin, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Wikstrom, M. / Wisniewska, M. / Schuler, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Human CTP:Phosphoethanolamine Cytidylyltransferase Authors: Karlberg, T. / Welin, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / ...Authors: Karlberg, T. / Welin, M. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Thorsell, A.G. / Tresaugues, L. / Van Den Berg, S. / Weigelt, J. / Wikstrom, M. / Wisniewska, M. / Schuler, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3elb.cif.gz | 77 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3elb.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 3elb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3elb_validation.pdf.gz | 775.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3elb_full_validation.pdf.gz | 777.3 KB | Display | |
Data in XML | 3elb_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 3elb_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/3elb ftp://data.pdbj.org/pub/pdb/validation_reports/el/3elb | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39118.121 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: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)R3 pRARE References: UniProt: Q99447, ethanolamine-phosphate cytidylyltransferase |
---|---|
#2: Chemical | ChemComp-C5P / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.93 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, 0.2M Mg-Formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97981, 0.97969, 0.97201 | ||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 21, 2008 / Details: mirrors | ||||||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 26706 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 16 | ||||||||||||
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3912 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2→19.74 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.812 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19.282 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
|