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Yorodumi- PDB-4yl7: Crystal structure of the indole prenyltransferase MpnD from Marin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yl7 | ||||||
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Title | Crystal structure of the indole prenyltransferase MpnD from Marinactinospora thermotolerans | ||||||
Components | Aromatic prenyltransferase | ||||||
Keywords | TRANSFERASE / PT-fold / indolactam V / indole prenyltransferase | ||||||
Function / homology | Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / alkaloid metabolic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / Aromatic prenyltransferase Function and homology information | ||||||
Biological species | Marinactinospora thermotolerans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å | ||||||
Authors | Mori, T. / Morita, H. / Abe, I. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Manipulation of prenylation reactions by structure-based engineering of bacterial indolactam prenyltransferases. Authors: Mori, T. / Zhang, L. / Awakawa, T. / Hoshino, S. / Okada, M. / Morita, H. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yl7.cif.gz | 91.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yl7.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 4yl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/4yl7 ftp://data.pdbj.org/pub/pdb/validation_reports/yl/4yl7 | HTTPS FTP |
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-Related structure data
Related structure data | 4ylaC 4yzjSC 4yzkC 4yzlC 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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Unit cell |
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-Components
#1: Protein | Mass: 41027.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinactinospora thermotolerans (bacteria) Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: I7EIW6 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris-HCl (pH8.5), 1470 mM (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 2, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 44641 / % possible obs: 99.6 % / Redundancy: 7.18 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.04 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 6.95 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 5.83 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YZJ Resolution: 1.601→34.139 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.13 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.601→34.139 Å
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Refine LS restraints |
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LS refinement shell |
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