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Yorodumi- PDB-5yk9: Crystal structure of selenomethionine-labelled indole prenyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yk9 | ||||||||||||
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Title | Crystal structure of selenomethionine-labelled indole prenyltransferase AmbP1 | ||||||||||||
Components | AmbP1 | ||||||||||||
Keywords | TRANSFERASE / cyanobacteria | ||||||||||||
Function / homology | Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metabolic process / AmbP1 Function and homology information | ||||||||||||
Biological species | Fischerella ambigua UTEX 1903 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.001 Å | ||||||||||||
Authors | Awakawa, T. / Nakashima, Y. / Liu, X. / Abe, I. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018 Title: Molecular Insight into the Mg2+-Dependent Allosteric Control of Indole Prenylation by Aromatic Prenyltransferase AmbP1 Authors: Awakawa, T. / Mori, T. / Nakashima, Y. / Zhai, R. / Wong, C.P. / Hillwig, M.L. / Liu, X. / Abe, I. #1: Journal: To Be Published Title: Crystal structure of selenomethionine-labelled indole prenyltransferase AmbP1 at 3.00 Angstroms resolution. Authors: Awakawa, T. / Nakashima, Y. / 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 | 5yk9.cif.gz | 117.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yk9.ent.gz | 96.1 KB | Display | PDB format |
PDBx/mmJSON format | 5yk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/5yk9 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/5yk9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35342.262 Da / Num. of mol.: 2 / Fragment: UNP residues 2-309 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fischerella ambigua UTEX 1903 (bacteria) Gene: ambP1, famD2 / Production host: Escherichia coli (E. coli) / References: UniProt: V5TDZ4 |
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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: 3.83 Å3/Da / Density % sol: 67.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG8000, MES, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.16 Å / Num. obs: 21912 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.513 / Num. unique obs: 2545 / Rpim(I) all: 0.213 / Rrim(I) all: 0.556 / Rsym value: 0.513 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.001→49.16 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 26.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.001→49.16 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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