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Yorodumi- PDB-3uj7: Phosphoethanolamine methyltransferase from Plasmodium falciparum ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uj7 | ||||||
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Title | Phosphoethanolamine methyltransferase from Plasmodium falciparum in complex with SAM and PO4 | ||||||
Components | Phosphoethanolamine N-methyltransferase | ||||||
Keywords | TRANSFERASE / Plasmodium / parasite / methyltransferase | ||||||
Function / homology | Function and homology information : / phosphoethanolamine N-methyltransferase activity / phosphoethanolamine N-methyltransferase / phosphatidylcholine biosynthetic process / methylation / Golgi membrane / Golgi apparatus Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 Å | ||||||
Authors | Lee, S.G. / Kim, Y. / Alpert, T.D. / Nagata, A. / Jez, J.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structure and reaction mechanism of phosphoethanolamine methyltransferase from the malaria parasite Plasmodium falciparum: an antiparasitic drug target. Authors: Lee, S.G. / Kim, Y. / Alpert, T.D. / Nagata, A. / Jez, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uj7.cif.gz | 239.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uj7.ent.gz | 192.6 KB | Display | PDB format |
PDBx/mmJSON format | 3uj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uj7_validation.pdf.gz | 943.2 KB | Display | wwPDB validaton report |
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Full document | 3uj7_full_validation.pdf.gz | 947.8 KB | Display | |
Data in XML | 3uj7_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 3uj7_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/3uj7 ftp://data.pdbj.org/pub/pdb/validation_reports/uj/3uj7 | HTTPS FTP |
-Related structure data
Related structure data | 3uj6C 3uj8C 3uj9C 3ujaC 3ujbC 3ujcC 3ujdC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31084.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PMT / Production host: Escherichia coli (E. coli) / References: UniProt: Q6T755 #2: Chemical | #3: Chemical | #4: 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: 2.29 Å3/Da / Density % sol: 46.35 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG-8000, 0.1 M sodium cacodylate, pH 6.5, 0.2 M sodium acetate, 5 mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2010 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.549→37.8 Å / Num. obs: 74087 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.067 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 1.55→1.6 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.382 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.549→37.774 Å / SU ML: 0.17 / σ(F): 0.03 / Phase error: 18.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.248 Å2 / ksol: 0.386 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.549→37.774 Å
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Refine LS restraints |
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LS refinement shell |
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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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