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Yorodumi- PDB-4dm3: Crystal structure of human PNMT in complex adohcy, resorcinol and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dm3 | ||||||
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Title | Crystal structure of human PNMT in complex adohcy, resorcinol and imidazole | ||||||
Components | Phenylethanolamine N-methyltransferase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information phenylethanolamine N-methyltransferase / phenylethanolamine N-methyltransferase activity / epinephrine biosynthetic process / Catecholamine biosynthesis / catecholamine biosynthetic process / methylation / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / PDB ENTRY 3KPY / Resolution: 2.4001 Å | ||||||
Authors | Nair, P.C. / Malde, A.K. / Mark, A.E. | ||||||
Citation | Journal: Biochem.J. / Year: 2010 Title: Fragment-based screening by X-ray crystallography, MS and isothermal titration calorimetry to identify PNMT (phenylethanolamine N-methyltransferase) inhibitors. Authors: Drinkwater, N. / Vu, H. / Lovell, K.M. / Criscione, K.R. / Collins, B.M. / Prisinzano, T.E. / Poulsen, S.A. / McLeish, M.J. / Grunewald, G.L. / Martin, J.L. | ||||||
History |
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Remark 0 | THIS ENTRY 4DM3 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R3KPYSF) ...THIS ENTRY 4DM3 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA (R3KPYSF) DETERMINED BY AUTHORS OF THE PDB ENTRY 3KPY: | ||||||
Remark 200 | AUTHOR USED THE SF DATA FROM ENTRY 3KPY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dm3.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dm3.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 4dm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/4dm3 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/4dm3 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 31845.967 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PNMT, PENT / Plasmid: pET17 PNMT-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P11086, phenylethanolamine N-methyltransferase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.45 % |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.563 Å / Num. obs: 30511 / % possible obs: 90.2 % / Redundancy: 4.91 % / Rmerge(I) obs: 0.096 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.276 / % possible all: 75 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.6_289) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: PDB ENTRY 3KPY / Resolution: 2.4001→45.563 Å / SU ML: 0.37 / σ(F): 1.33 / Phase error: 27.84 / 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 / Bsol: 33.245 Å2 / ksol: 0.319 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4001→45.563 Å
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Refine LS restraints |
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LS refinement shell |
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