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Yorodumi- PDB-4yla: Crystal structure of the indole prenyltransferase MpnD complexed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yla | |||||||||
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Title | Crystal structure of the indole prenyltransferase MpnD complexed with indolactam V and DMSPP | |||||||||
Components | Aromatic prenyltransferase | |||||||||
Keywords | TRANSFERASE / indole prenyltransferase / PT-fold / indolactam V | |||||||||
Function / homology | Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / alkaloid metabolic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / DIMETHYLALLYL S-THIOLODIPHOSPHATE / Chem-ILV / Aromatic prenyltransferase Function and homology information | |||||||||
Biological species | Marinactinospora thermotolerans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 | 4yla.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yla.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 4yla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/4yla ftp://data.pdbj.org/pub/pdb/validation_reports/yl/4yla | HTTPS FTP |
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-Related structure data
Related structure data | 4yl7C 4yzjSC 4yzkC 4yzlC C: citing same article (ref.) S: Starting model for refinement |
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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: Chemical | ChemComp-ILV / ( | ||||
#3: Chemical | #4: Chemical | ChemComp-DST / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.73 % |
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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 (NH)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2014 |
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: 1.4→50 Å / Num. obs: 66872 / % possible obs: 99.7 % / Redundancy: 6.98 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.83 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.03 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YZJ Resolution: 1.4→41.861 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.4 / 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: 1.4→41.861 Å
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Refine LS restraints |
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LS refinement shell |
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