+Open data
-Basic information
Entry | Database: PDB / ID: 3reo | ||||||
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Title | Monolignol O-methyltransferase (MOMT) | ||||||
Components | (Iso)eugenol O-methyltransferase(Iso)eugenol O-methyltransferase | ||||||
Keywords | TRANSFERASE / directed evolution / SATURATION MUTAGENESIS / regioselectivity | ||||||
Function / homology | Function and homology information (iso)eugenol O-methyltransferase / (iso)eugenol O-methyltransferase activity / S-adenosyl-L-methionine:eugenol-O-methyltransferase activity / organic substance metabolic process / methylation / protein dimerization activity Similarity search - Function | ||||||
Biological species | Clarkia breweri (fairy fans) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Bhuiya, M.W. / Liu, C.J. | ||||||
Citation | Journal: To be Published Title: Monolignol O-methyltransferase (MOMT) Authors: Bhuiya, M.W. / Liu, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3reo.cif.gz | 278.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3reo.ent.gz | 224.7 KB | Display | PDB format |
PDBx/mmJSON format | 3reo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/3reo ftp://data.pdbj.org/pub/pdb/validation_reports/re/3reo | HTTPS FTP |
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-Related structure data
Related structure data | 1kyzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | ( Mass: 39994.152 Da / Num. of mol.: 4 / Mutation: T133L, E165I, F175I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clarkia breweri (fairy fans) / Gene: IEMT1 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 References: UniProt: O04385, (iso)eugenol O-methyltransferase #2: Chemical | ChemComp-SAH / #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: 2.13 Å3/Da / Density % sol: 42.24 % |
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Crystal grow | Temperature: 295 K / pH: 6.8 Details: 26% PEG 4000, 0.3M magnesium nitrate,3% ethylene glycol, and 2 mM DTT , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 103127 / % possible obs: 97.1 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KYZ Resolution: 1.9→44.37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.583 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE IDENTITY OF THE LIGAND ON CHAINS B-D IS MOST LIKELY EUG. THE AUTHOR INDICATES THAT THE 2FO-FC ELECTRON DENSITY MAP IS NOT VERY CLEAR AND THAT THE LIGAND WAS BUILT USING AN OMIT MAP. ...Details: THE IDENTITY OF THE LIGAND ON CHAINS B-D IS MOST LIKELY EUG. THE AUTHOR INDICATES THAT THE 2FO-FC ELECTRON DENSITY MAP IS NOT VERY CLEAR AND THAT THE LIGAND WAS BUILT USING AN OMIT MAP. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→44.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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