[English] 日本語
Yorodumi- PDB-3hce: Crystal Structure of E185D hPNMT in Complex With Octopamine and AdoHcy -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hce | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of E185D hPNMT in Complex With Octopamine and AdoHcy | ||||||
Components | Phenylethanolamine N-methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase / Catecholamine biosynthesis / Polymorphism / S-adenosyl-L-methionine | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.85 Å | ||||||
Authors | Drinkwater, N. / Martin, J.L. | ||||||
Citation | Journal: Biochem.J. / Year: 2009 Title: Molecular recognition of physiological substrate noradrenaline by the adrenaline-synthesizing enzyme PNMT and factors influencing its methyltransferase activity. Authors: Drinkwater, N. / Gee, C.L. / Puri, M. / Criscione, K.R. / McLeish, M.J. / Grunewald, G.L. / Martin, J.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3hce.cif.gz | 224.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3hce.ent.gz | 181.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hce_validation.pdf.gz | 946.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3hce_full_validation.pdf.gz | 958 KB | Display | |
Data in XML | 3hce_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 3hce_validation.cif.gz | 31.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/3hce ftp://data.pdbj.org/pub/pdb/validation_reports/hc/3hce | HTTPS FTP |
-Related structure data
Related structure data | 3hcaC 3hcbC 3hccC 3hcdC 3hcfC 1hnnS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31831.939 Da / Num. of mol.: 2 / Mutation: E185D 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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.88 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG6K, LiCl, cacodylate, pH 5.8, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95667 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95667 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 20186 / Redundancy: 7.5 % / Biso Wilson estimate: 50.35 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1HNN Resolution: 2.85→45.445 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.828 / SU ML: 0.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.07 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.201 Å2 / ksol: 0.288 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.35 Å2 / Biso mean: 52.524 Å2 / Biso min: 14.27 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→45.445 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 24.1876 Å / Origin y: 51.3494 Å / Origin z: -5.2075 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|