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- PDB-3abw: Crystal structure of pharaonis halorhodopsin in complex with azide ion -
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Open data
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Basic information
Entry | Database: PDB / ID: 3abw | ||||||
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Title | Crystal structure of pharaonis halorhodopsin in complex with azide ion | ||||||
![]() | Halorhodopsin | ||||||
![]() | MEMBRANE PROTEIN / LIGHT-DRIVEN CHLORIDE ION PUMP / TRIMERIC BACTERIORUBERIN-PROTEIN COMPLEX / RETINAL PROTEIN | ||||||
Function / homology | Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha / BACTERIORUBERIN / AZIDE ION / Chem-L3P / RETINAL / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kouyama, T. / Kanada, S. | ||||||
![]() | ![]() Title: Binding mode of azide ion to pharaonis halorhodopsin Authors: Kanada, S. / Kouyama, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.9 KB | Display | ![]() |
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PDB format | ![]() | 131.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 35.7 KB | Display | |
Data in CIF | ![]() | 46.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a7kS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABD
#1: Protein | Mass: 30975.096 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: STRAIN MK-1 WAS A HALORHODOPSIN-OVERPRODUCING MUTANT GENERATED FROM TYPE STRAIN D2160T. Source: (natural) ![]() |
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-Non-polymers , 5 types, 145 molecules ![](data/chem/img/RET.gif)
![](data/chem/img/22B.gif)
![](data/chem/img/L3P.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/22B.gif)
![](data/chem/img/L3P.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-L3P / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.52 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6 Details: A DROP CONTAINING 2MG/ML Halorhodopsin, 1M AMMONIUM SULFATE, 0.16M NACL, 0.04M Na-citrate, 0.04% NAN3,5MG/ML NONYL GLUCOSIDE WAS CONCENTRATED BY VAPOR DIFFUSIONAGAINST A RESERVE SOLUTION ...Details: A DROP CONTAINING 2MG/ML Halorhodopsin, 1M AMMONIUM SULFATE, 0.16M NACL, 0.04M Na-citrate, 0.04% NAN3,5MG/ML NONYL GLUCOSIDE WAS CONCENTRATED BY VAPOR DIFFUSIONAGAINST A RESERVE SOLUTION CONTAINING 2.9 M AMMONIUM SULFATE, 0.04M Na-citrate, PH 6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 288K. After the crystal grew, the mother solution was exchanged with a solution containing 3M Ammonium sulfate, 200 mM Na-N3, 100 mM HEPES (pH7) and 30 % trehalose. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 14, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.15 Å / Num. all: 91795 / Num. obs: 80799 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.526 / % possible all: 74.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3a7k Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 99.0968 Å2 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.4952 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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LS refinement shell |
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Xplor file |
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