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Yorodumi- PDB-4mik: Crystal Structure of hPNMT in Complex with bisubstrate inhibitor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mik | ||||||
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Title | Crystal Structure of hPNMT in Complex with bisubstrate inhibitor (2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-(((2-(((7-nitro-1,2,3,4-tetrahydroisoquinolin-3-yl)methyl)amino)ethyl)thio)methyl)tetrahydrofuran-3,4-diol | ||||||
Components | Phenylethanolamine N-methyltransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / methyltransferase / adrenaline synthesis / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9506 Å | ||||||
Authors | Bart, A.G. / Scott, E.E. | ||||||
Citation | Journal: To be Published Title: To be published Authors: Bart, A.G. / Scott, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mik.cif.gz | 206.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mik.ent.gz | 175.5 KB | Display | PDB format |
PDBx/mmJSON format | 4mik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mik_validation.pdf.gz | 962.8 KB | Display | wwPDB validaton report |
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Full document | 4mik_full_validation.pdf.gz | 973.3 KB | Display | |
Data in XML | 4mik_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 4mik_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/4mik ftp://data.pdbj.org/pub/pdb/validation_reports/mi/4mik | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: pET17PNMT-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysE 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: 3.31 Å3/Da / Density % sol: 62.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Na cacodylate pH 5.6, 0.17 M LiCl, 9% PEG 6000, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2013 / Details: RH COATED MIRROR, K-B FOCUSING MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→38.62 Å / Num. all: 63110 / Num. obs: 63010 / % possible obs: 99.8 % / Redundancy: 25.6 % |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 24.7 % / Mean I/σ(I) obs: 1.7 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9506→38.617 Å / SU ML: 0.24 / Phase error: 24.91 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9506→38.617 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: 23
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