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Yorodumi- PDB-3hcf: Crystal Structure of hPNMT in Complex With 3-trifluoromethyl phen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hcf | ||||||
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Title | Crystal Structure of hPNMT in Complex With 3-trifluoromethyl phenylethanolamine 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: 2.702 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hcf.cif.gz | 225.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hcf.ent.gz | 182.9 KB | Display | PDB format |
PDBx/mmJSON format | 3hcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hcf_validation.pdf.gz | 967.9 KB | Display | wwPDB validaton report |
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Full document | 3hcf_full_validation.pdf.gz | 979.8 KB | Display | |
Data in XML | 3hcf_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | 3hcf_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/3hcf ftp://data.pdbj.org/pub/pdb/validation_reports/hc/3hcf | HTTPS FTP |
-Related structure data
Related structure data | 3hcaC 3hcbC 3hccC 3hcdC 3hceC 1hnnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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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 | ChemComp-EDO / | #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: 3.22 Å3/Da / Density % sol: 61.78 % |
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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 |
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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: 2.7→41.84 Å / Num. obs: 23386 / Redundancy: 9.8 % / Biso Wilson estimate: 58.24 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1HNN Resolution: 2.702→41.84 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.802 / SU ML: 0.35 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.07 / 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: 32.718 Å2 / ksol: 0.291 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 165.26 Å2 / Biso mean: 63.572 Å2 / Biso min: 18.43 Å2
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Refinement step | Cycle: LAST / Resolution: 2.702→41.84 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: 24.0778 Å / Origin y: 51.2364 Å / Origin z: -5.3465 Å
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Refinement TLS group |
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