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Yorodumi- PDB-1n7j: The structure of Phenylethanolamine N-methyltransferase in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n7j | ||||||
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Title | The structure of Phenylethanolamine N-methyltransferase in complex with S-adenosylhomocysteine and an iodinated inhibitor | ||||||
Components | Phenylethanolamine N-methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase / catecholamine / adrenaline / epinephrine / s-adenosylmethionine / s-adenolsylhomocysteine | ||||||
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 / difference fourier / Resolution: 2.7 Å | ||||||
Authors | McMillan, F.M. / Archbold, J. / McLeish, M.J. / Caine, J.M. / Criscione, K.R. / Grunewald, G.L. / Martin, J.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 Title: Molecular recognition of sub-micromolar inhibitors by the epinephrine-synthesizing enzyme phenylethanolamine N-methyltransferase. Authors: McMillan, F.M. / Archbold, J. / McLeish, M.J. / Caine, J.M. / Criscione, K.R. / 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 | 1n7j.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n7j.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 1n7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n7j_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1n7j_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 1n7j_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 1n7j_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/1n7j ftp://data.pdbj.org/pub/pdb/validation_reports/n7/1n7j | HTTPS FTP |
-Related structure data
Related structure data | 1n7iC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30887.982 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PNMT OR PENT / Plasmid: pET17 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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: 3.53 Å3/Da / Density % sol: 64.86 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6K, lithium chloride, cacodylate , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.25 / PH range high: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 28, 1997 / Details: yale mirrors |
Radiation | Monochromator: nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→31.39 Å / Num. all: 22078 / Num. obs: 22078 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.36 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.1 / % possible all: 77 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 50 Å / Num. measured all: 52232 |
Reflection shell | *PLUS % possible obs: 77 % |
-Processing
Software |
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Refinement | Method to determine structure: difference fourier Starting model: 1HNN Resolution: 2.7→31.39 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 1521446.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 18.394 Å2 / ksol: 0.292118 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.3 Å2
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Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→31.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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