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Yorodumi- PDB-3hl4: Crystal structure of a mammalian CTP:phosphocholine cytidylyltran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hl4 | ||||||
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Title | Crystal structure of a mammalian CTP:phosphocholine cytidylyltransferase with CDP-choline | ||||||
Components | Choline-phosphate cytidylyltransferase A | ||||||
Keywords | TRANSFERASE / Cytidylyltransferase / Rossmann Fold / Phospholipid synthesis / Phosphatidylcholine / Phosphocholine / CTP / CDP-choline / Amphitropic protein / Lipid metabolism / Nucleotidyltransferase / Phosphoprotein | ||||||
Function / homology | Function and homology information Synthesis of PC / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / CDP-choline pathway / glycogen granule / phosphatidylcholine biosynthetic process / phosphatidylcholine binding / extrinsic component of membrane / molecular function inhibitor activity / nuclear envelope ...Synthesis of PC / choline-phosphate cytidylyltransferase / choline-phosphate cytidylyltransferase activity / CDP-choline pathway / glycogen granule / phosphatidylcholine biosynthetic process / phosphatidylcholine binding / extrinsic component of membrane / molecular function inhibitor activity / nuclear envelope / calmodulin binding / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Lee, J. / Paetzel, M. / Cornell, R.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal Structure of a mammalian CTP: Phosphocholine cytidylyltransferase catalytic domain reveals novel active site residues within a highly conserved nucleotidyl-transferase fold Authors: Lee, J. / Johnson, J.E. / Ding, Z. / Paetzel, M. / Cornell, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hl4.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hl4.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/3hl4 ftp://data.pdbj.org/pub/pdb/validation_reports/hl/3hl4 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Biological unit is a dimer in ASU |
-Components
#1: Protein | Mass: 26792.066 Da / Num. of mol.: 2 / Fragment: Domain N and C / Mutation: None Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ctpct, Pcyt1, Pcyt1a / Plasmid: PVL1393 / Production host: TRICHOPLUSIA NI (cabbage looper) References: UniProt: P19836, choline-phosphate cytidylyltransferase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Na Acetate 1.4M Na Formate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2005 / Details: KOHZU: Double Crystal Si(111) |
Radiation | Monochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 26316 / Num. obs: 26316 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 32.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 6.6 / Num. unique all: 2587 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.862 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.213 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.857 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.201→2.258 Å / Total num. of bins used: 20
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