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Yorodumi- PDB-2an3: Structure of PNMT with S-adenosyl-L-homocysteine and the semi-rig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2an3 | ||||||
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Title | Structure of PNMT with S-adenosyl-L-homocysteine and the semi-rigid analogue acceptor substrate cis-(1R,2S)-2-amino-1-tetralol. | ||||||
Components | Phenylethanolamine N-methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase / substrate structure / S-adenosyl-L-methionine / adrenaline synthesis | ||||||
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: 2.2 Å | ||||||
Authors | Gee, C.L. / Tyndall, J.D.A. / Grunewald, G.L. / Wu, Q. / McLeish, M.J. / Martin, J.L. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Mode of binding of methyl acceptor substrates to the adrenaline-synthesizing enzyme phenylethanolamine N-methyltransferase: implications for catalysis Authors: Gee, C.L. / Tyndall, J.D.A. / 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 | 2an3.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2an3.ent.gz | 95.9 KB | Display | PDB format |
PDBx/mmJSON format | 2an3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2an3_validation.pdf.gz | 974.9 KB | Display | wwPDB validaton report |
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Full document | 2an3_full_validation.pdf.gz | 980.8 KB | Display | |
Data in XML | 2an3_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 2an3_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/2an3 ftp://data.pdbj.org/pub/pdb/validation_reports/an/2an3 | HTTPS FTP |
-Related structure data
Related structure data | 2an4C 2an5C 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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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | enzyme is active as a monomer |
-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 / Plasmid: pET17PNMT-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: 3.1 Å3/Da / Density % sol: 60.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG 6000, LiCl, cacodylate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 24, 2004 / Details: Osmic mirrors (Maxscreen) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→66.31 Å / Num. all: 43227 / Num. obs: 42859 / % possible obs: 99.2 % / Redundancy: 6.67 % / Rmerge(I) obs: 0.079 / Χ2: 0.98 / Net I/σ(I): 12.8 / Scaling rejects: 2162 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible obs: 99.4 % / Redundancy: 6.28 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.7 / Num. measured obs: 68 / Num. unique all: 4230 / Χ2: 1.18 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1HNN Resolution: 2.2→66.31 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 50.5 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.365 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→66.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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