+Open data
-Basic information
Entry | Database: PDB / ID: 3kpj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of hPNMT in Complex AdoHcy and Bound Phosphate | ||||||
Components | Phenylethanolamine N-methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase / fragment screening / Catecholamine biosynthesis / 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 / FOURIER SYNTHESIS / Resolution: 2.5 Å | ||||||
Authors | Drinkwater, N. / Martin, J.L. | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3kpj.cif.gz | 225.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3kpj.ent.gz | 183.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/3kpj ftp://data.pdbj.org/pub/pdb/validation_reports/kp/3kpj | HTTPS FTP |
---|
-Related structure data
Related structure data | 3kpuC 3kpvC 3kpwC 3kpyC 3kqmC 3kqoC 3kqpC 3kqqC 3kqsC 3kqtC 3kqvC 3kqwC 3kqyC 3kr0C 3kr1C 3kr2C 1hnnS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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: PENT, PNMT / 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: 3.27 Å3/Da / Density % sol: 62.39 % |
---|---|
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: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 3, 2007 |
Radiation | Monochromator: HiRes2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→33.38 Å / Num. obs: 29790 / % possible obs: 99.1 % / Redundancy: 3.77 % / Rmerge(I) obs: 0.05 / Χ2: 0.97 / Net I/σ(I): 11.7 / Scaling rejects: 850 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.2 / Num. measured all: 11110 / Num. unique all: 2933 / Χ2: 1.16 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1HNN Resolution: 2.5→33.383 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.765 / SU ML: 0.42 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0.01 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.753 Å2 / ksol: 0.312 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 135.66 Å2 / Biso mean: 76.645 Å2 / Biso min: 42.63 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→33.383 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 24.2957 Å / Origin y: 51.7534 Å / Origin z: -5.048 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|