[English] 日本語
Yorodumi- PDB-5zoh: Crystal structure of a far-red light-absorbing form of AnPixJg2_B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zoh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a far-red light-absorbing form of AnPixJg2_BV4 in complex with biliverdin | ||||||
Components | Methyl-accepting chemotaxis protein | ||||||
Keywords | SIGNALING PROTEIN / Photoreceptor / Cyanobacteriochrome / Complex / Tetrapyrrole / Biliverdin | ||||||
Function / homology | Function and homology information transmembrane signaling receptor activity / chemotaxis / signal transduction / membrane Similarity search - Function | ||||||
Biological species | Nostoc sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Miyazaki, T. / Fushimi, K. / Narikawa, R. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Rational conversion of chromophore selectivity of cyanobacteriochromes to accept mammalian intrinsic biliverdin. Authors: Fushimi, K. / Miyazaki, T. / Kuwasaki, Y. / Nakajima, T. / Yamamoto, T. / Suzuki, K. / Ueda, Y. / Miyake, K. / Takeda, Y. / Choi, J.H. / Kawagishi, H. / Park, E.Y. / Ikeuchi, M. / Sato, M. / Narikawa, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5zoh.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5zoh.ent.gz | 37.5 KB | Display | PDB format |
PDBx/mmJSON format | 5zoh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zoh_validation.pdf.gz | 766.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5zoh_full_validation.pdf.gz | 771.9 KB | Display | |
Data in XML | 5zoh_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 5zoh_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/5zoh ftp://data.pdbj.org/pub/pdb/validation_reports/zo/5zoh | HTTPS FTP |
-Related structure data
Related structure data | 3w2zS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22641.479 Da / Num. of mol.: 1 / Mutation: H293Y, F308T, H318Y, I336V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all1069 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q8YXY7 |
---|---|
#2: Chemical | ChemComp-BLA / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.04 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.1 M sodium cacodylate, 26% PEG 3350, 0.2 M ammonium sulfate PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 27039 / % possible obs: 98 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2737 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W2Z Resolution: 1.6→31.67 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 1.881 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.308 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→31.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|