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- PDB-3ddl: Crystallographic Structure of Xanthorhodopsin, a Light-Driven Ion... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ddl | ||||||
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Title | Crystallographic Structure of Xanthorhodopsin, a Light-Driven Ion Pump with Dual Chromophore | ||||||
![]() | Xanthorhodopsin | ||||||
![]() | TRANSPORT PROTEIN / rhodopsin / carotenoid / ion pump / light-harvesting / antenna / retinal | ||||||
Function / homology | ![]() light-activated monoatomic ion channel activity / : / phototransduction / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Stagno, J. / Luecke, H. / Schobert, B. / Lanyi, J.K. / Imasheva, E.S. / Wang, J.M. / Balashov, S.P. | ||||||
![]() | ![]() Title: Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore. Authors: Luecke, H. / Schobert, B. / Stagno, J. / Imasheva, E.S. / Wang, J.M. / Balashov, S.P. / Lanyi, J.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.4 KB | Display | ![]() |
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PDB format | ![]() | 96.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30105.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 89 molecules ![](data/chem/img/SXN.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/PX4.gif)
![](data/chem/img/PCW.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/PX4.gif)
![](data/chem/img/PCW.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-UNL / Num. of mol.: 21 / Source method: obtained synthetically #4: Chemical | #5: Chemical | ChemComp-PX4 / | #6: Chemical | ChemComp-PCW / | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE HETERO GROUPS UNL 402-409 CHAIN A AND UNL 402-414 CHAIN B ARE CARBON CHAINS THAT REPRESENT ...THE HETERO GROUPS UNL 402-409 CHAIN A AND UNL 402-414 CHAIN B ARE CARBON CHAINS THAT REPRESENT FATTY ACID CHAINS OF PHOSPHOLIP |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.03 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 5mg/ml xanthorhodopsin in 30mM phosphate pH 5.6, 1mM Na azide was solubilized in 1/3 volume of 16.7% dimyristoyl phoshatidylcholine in 20% nonyl maltoside. Crystals grew in 2.5-3M Na ...Details: 5mg/ml xanthorhodopsin in 30mM phosphate pH 5.6, 1mM Na azide was solubilized in 1/3 volume of 16.7% dimyristoyl phoshatidylcholine in 20% nonyl maltoside. Crystals grew in 2.5-3M Na phosphate, pH 5.6, 2.5 mM Na azide after 3-4 months, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→45.1 Å / Num. obs: 46289 / % possible obs: 94.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Χ2: 0.99 / Net I/σ(I): 8.4 / Scaling rejects: 1260 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Resolution: 1.9→45.1 Å / FOM work R set: 0.712 / σ(F): 0
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Solvent computation | Bsol: 97.153 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.446 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→45.1 Å
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Refine LS restraints |
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Xplor file |
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