[English] 日本語
Yorodumi- PDB-6kmd: Crystal structure of SeMet-phytochromobilin synthase from tomato ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kmd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of SeMet-phytochromobilin synthase from tomato in complex with biliverdin | ||||||
Components | Phytochromobilin synthase | ||||||
Keywords | OXIDOREDUCTASE / Substrate complex | ||||||
Function / homology | Function and homology information phytochromobilin:ferredoxin oxidoreductase / chloroplast-nucleus signaling pathway / phytochromobilin:ferredoxin oxidoreductase activity / phytochromobilin biosynthetic process / cobalt ion binding / chloroplast Similarity search - Function | ||||||
Biological species | Solanum lycopersicum (tomato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Sugishima, M. / Wada, K. / Fukuyama, K. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Crystal structure of phytochromobilin synthase in complex with biliverdin IX alpha , a key enzyme in the biosynthesis of phytochrome. Authors: Sugishima, M. / Wada, K. / Fukuyama, K. / Yamamoto, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6kmd.cif.gz | 136.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6kmd.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 6kmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/6kmd ftp://data.pdbj.org/pub/pdb/validation_reports/km/6kmd | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37005.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: AUREA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: Q588D6, phytochromobilin:ferredoxin oxidoreductase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-BLA / | ||||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.83 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 8000, magnesium chloride, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.975 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.77 Å / Num. obs: 31770 / % possible obs: 99.8 % / Redundancy: 6.97 % / CC1/2: 0.997 / Net I/σ(I): 13.21 |
Reflection shell | Resolution: 2.2→2.33 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.88 / Num. unique obs: 5053 / CC1/2: 0.864 / % possible all: 98.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.2→43.4756 Å / Cross valid method: THROUGHOUT Details: For the model refinement, Bijvoet pairs were merged.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→43.4756 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.3 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|