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Yorodumi- PDB-3hcb: Crystal Structure of hPNMT in Complex With Noradrenochrome and AdoHcy -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hcb | ||||||
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Title | Crystal Structure of hPNMT in Complex With Noradrenochrome 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 / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Authors | Drinkwater, N. / Martin, J.L. / Gee, C.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 | 3hcb.cif.gz | 229.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hcb.ent.gz | 185.3 KB | Display | PDB format |
PDBx/mmJSON format | 3hcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hcb_validation.pdf.gz | 952.8 KB | Display | wwPDB validaton report |
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Full document | 3hcb_full_validation.pdf.gz | 960.1 KB | Display | |
Data in XML | 3hcb_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 3hcb_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/3hcb ftp://data.pdbj.org/pub/pdb/validation_reports/hc/3hcb | HTTPS FTP |
-Related structure data
Related structure data | 3hcaC 3hccC 3hcdC 3hceC 3hcfC 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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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: 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: 3.27 Å3/Da / Density % sol: 62.42 % |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 25, 2004 |
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: 2.4→66.5 Å / Num. obs: 33903 / Redundancy: 7.85 % / Biso Wilson estimate: 45.07 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.4→2.43 Å / Redundancy: 7.78 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 4.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1HNN Resolution: 2.4→66.5 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.832 / SU ML: 0.36 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.34 / 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: 58.115 Å2 / ksol: 0.346 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.12 Å2 / Biso mean: 49 Å2 / Biso min: 23.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→66.5 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: 24
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Refinement TLS params. | Method: refined / Origin x: 24.2652 Å / Origin y: 51.2577 Å / Origin z: -5.462 Å
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Refinement TLS group |
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