+Open data
-Basic information
Entry | Database: PDB / ID: 5y4g | ||||||
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Title | Apo Structure of AmbP3 | ||||||
Components | AmbP3 | ||||||
Keywords | TRANSFERASE / Prenyltransferase | ||||||
Function / homology | Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metabolic process / AmbP3 Function and homology information | ||||||
Biological species | Fischerella ambigua UTEX 1903 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 5y4g.cif.gz | 136.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y4g.ent.gz | 105.2 KB | Display | PDB format |
PDBx/mmJSON format | 5y4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/5y4g ftp://data.pdbj.org/pub/pdb/validation_reports/y4/5y4g | HTTPS FTP |
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-Related 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: 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 (E. coli) / References: UniProt: V5TDY7 #2: 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: 2.51 Å3/Da / Density % sol: 51.01 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, magnesium chloride, PEG 8000 |
-Data collection
Diffraction | Mean temperature: 277 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: Dec 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.9 Å / Num. obs: 45559 / % possible obs: 97.5 % / Redundancy: 3.5 % / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.159 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→31.987 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→31.987 Å
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Refine LS restraints |
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LS refinement shell |
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