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Yorodumi- PDB-2opb: Structure of K57A hPNMT with inhibitor 3-fluoromethyl-7-thiomorph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2opb | ||||||
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Title | Structure of K57A hPNMT with inhibitor 3-fluoromethyl-7-thiomorpholinosulfonamide-THIQ and AdoHcy | ||||||
Components | Phenylethanolamine N-methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase | ||||||
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: 2.8 Å | ||||||
Authors | Drinkwater, N. / Martin, J.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2007 Title: Enzyme Adaptation to Inhibitor Binding: A Cryptic Binding Site in Phenylethanolamine N-Methyltransferase. Authors: Gee, C.L. / Drinkwater, N. / Tyndall, J.D. / Grunewald, G.L. / Wu, Q. / McLeish, M.J. / 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 | 2opb.cif.gz | 120 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2opb.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 2opb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2opb_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2opb_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2opb_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 2opb_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/2opb ftp://data.pdbj.org/pub/pdb/validation_reports/op/2opb | HTTPS FTP |
-Related structure data
Related structure data | 2g70C 2g71C 2g72C 2obfC 2onyC 2onzC 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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Details | the biological unit is a monomer |
-Components
#1: Protein | Mass: 31787.865 Da / Num. of mol.: 2 / Mutation: K57A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PNMT, PENT / Plasmid: 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-PO4 / | #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: 3.29 Å3/Da / Density % sol: 62.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 8% PEG6K, 0.25 M LiCl, 0.1 M cacodylate, pH 5.8, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 22, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→66.77 Å / Num. obs: 21616 / % possible obs: 99.8 % / Redundancy: 7.06 % / Rmerge(I) obs: 0.114 / Χ2: 0.89 / Net I/σ(I): 7.7 / Scaling rejects: 1155 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1,2
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1HNN Resolution: 2.8→54.4 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 647660.75 / 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: 46.248 Å2 / ksol: 0.316 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→54.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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