+Open data
-Basic information
Entry | Database: PDB / ID: 1x0i | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Acid Blue Form of Bacteriorhodopsin | ||||||
Components | Bacteriorhodopsin | ||||||
Keywords | PROTON TRANSPORT / 7 transmembrane helices / membrane protein | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | Halobacterium salinarum (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Okumura, H. / Murakami, M. / Kouyama, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal Structures of Acid Blue and Alkaline Purple Forms of Bacteriorhodopsin Authors: Okumura, H. / Murakami, M. / Kouyama, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1x0i.cif.gz | 102.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1x0i.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 1x0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/1x0i ftp://data.pdbj.org/pub/pdb/validation_reports/x0/1x0i | HTTPS FTP |
---|
-Related structure data
Related structure data | 1x0kC 1iw6S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Number of models | 2 |
-Components
-Protein , 1 types, 1 molecules 1
#1: Protein | Mass: 26814.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: JW3 / References: UniProt: P02945 |
---|
-Non-polymers , 5 types, 31 molecules
#2: Chemical | ChemComp-SO4 / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-RET / | ||||
#4: Chemical | #5: Chemical | ChemComp-L2P / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 40 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 2 Details: ammonium sulfate, pH 2.00, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 28, 2004 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→54.52 Å / Num. all: 15620 / Num. obs: 15527 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 45 Å2 / Limit h max: 38 / Limit h min: 0 / Limit k max: 22 / Limit k min: 0 / Limit l max: 47 / Limit l min: 0 / Observed criterion F max: 2176769.36 / Observed criterion F min: 20.1 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2216 / Rsym value: 0.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1iw6 Resolution: 2.3→14.91 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 84.2683 Å2 / ksol: 0.413201 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 158.02 Å2 / Biso mean: 43.54 Å2 / Biso min: 15.84 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→14.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
|