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- PDB-5yk9: Crystal structure of selenomethionine-labelled indole prenyltrans... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yk9 | ||||||||||||
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Title | Crystal structure of selenomethionine-labelled indole prenyltransferase AmbP1 | ||||||||||||
![]() | AmbP1 | ||||||||||||
![]() | TRANSFERASE / cyanobacteria | ||||||||||||
Function / homology | Aromatic prenyltransferase, CloQ-type / Prenyltransferase-like superfamily / Aromatic prenyltransferase Orf2 / Aromatic prenyltransferase / prenyltransferase activity / metabolic process / metal ion binding / AmbP1![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Awakawa, T. / Nakashima, Y. / Liu, X. / Abe, I. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.8 KB | Display | ![]() |
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PDB format | ![]() | 96.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.3 KB | Display | ![]() |
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Full document | ![]() | 440.8 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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.) ![]() Gene: ambP1, famD2 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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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