+Open data
-Basic information
Entry | Database: PDB / ID: 5y7c | |||||||||
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Title | Hapalindole A and DMSPP Bound AmbP3 | |||||||||
Components | AmbP3 | |||||||||
Keywords | TRANSFERASE / Prenyltransferase | |||||||||
Function / homology | Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metabolic process / Hapalindole A / DIMETHYLALLYL S-THIOLODIPHOSPHATE / AmbP3 Function and homology information | |||||||||
Biological species | Fischerella ambigua UTEX 1903 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å | |||||||||
Authors | Wong, C.P. / Awakawa, T. / Nakashima, Y. | |||||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018 Title: Two Distinct Substrate Binding Modes for the Normal and Reverse Prenylation of Hapalindoles by the Prenyltransferase AmbP3 Authors: Wong, C.P. / Awakawa, T. / Nakashima, Y. / Mori, T. / Zhu, Q. / Liu, X. / Abe, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y7c.cif.gz | 135 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y7c.ent.gz | 101.9 KB | Display | PDB format |
PDBx/mmJSON format | 5y7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/5y7c ftp://data.pdbj.org/pub/pdb/validation_reports/y7/5y7c | HTTPS FTP |
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-Related structure data
Related structure data | 5y4gSC 5y72C 5y84C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38044.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria) Gene: ambP3 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: V5TDY7 #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: 2.34 Å3/Da / Density % sol: 47.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, PEG 8000, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.2 Å / Num. obs: 45052 / % possible obs: 97.2 % / Redundancy: 3.5 % / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.476 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y4G Resolution: 2.003→37.837 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.003→37.837 Å
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Refine LS restraints |
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LS refinement shell |
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