[English] 日本語
Yorodumi- PDB-1or4: Crystal Structure of HemAT sensor domain from B.subtilis in the c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1or4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of HemAT sensor domain from B.subtilis in the cyano-liganded form | ||||||
Components | Heme-based aerotactic transducer hemAT | ||||||
Keywords | SIGNALING PROTEIN / Globin fold | ||||||
Function / homology | Function and homology information aerotaxis / oxygen binding / heme binding / signal transduction / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å | ||||||
Authors | Zhang, W. / Phillips Jr., G.N. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structure of the oxygen sensor in Bacillus subtilis: signal transduction of chemotaxis by control of symmetry. Authors: Zhang, W. / Phillips, G.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1or4.cif.gz | 89 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1or4.ent.gz | 67.8 KB | Display | PDB format |
PDBx/mmJSON format | 1or4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/1or4 ftp://data.pdbj.org/pub/pdb/validation_reports/or/1or4 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20841.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yhfV / Plasmid: pET29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O07621 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.9 % | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium citrate, KH2PO4, n-Octyl-D-glucoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2002 | ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.15→100 Å / Num. all: 31839 / Num. obs: 31839 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||||||||
Reflection shell | Resolution: 2.15→2.23 Å / % possible all: 83.7 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 27 Å / Num. obs: 18722 / Num. measured all: 83301 / Rmerge(I) obs: 0.063 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 83.7 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 5.35 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.15→26.98 Å / Num. parameters: 12286 / Num. restraintsaints: 12870 / Cross valid method: FREE R / σ(F): 0 / Details: ANISOTROPIC REFINEMENT APPLIED TO HEME GROUP ONLY
| |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å / Num. disordered residues: 4 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2901.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→26.98 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 27 Å / Rfactor Rwork: 0.197 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|