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Open data
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Basic information
Entry | Database: PDB / ID: 1c8s | ||||||
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Title | BACTERIORHODOPSIN D96N LATE M STATE INTERMEDIATE | ||||||
![]() | BACTERIORHODOPSIN ("M" STATE INTERMEDIATE) | ||||||
![]() | ION TRANSPORT / ION PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / LIPIDS / PHOTORECEPTOR / HALOARCHAEA / D96N M INTERMEDIATE / MEROHEDRAL TWINNING | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Luecke, H. | ||||||
![]() | ![]() Title: Structural changes in bacteriorhodopsin during ion transport at 2 angstrom resolution. Authors: Luecke, H. / Schobert, B. / Richter, H.T. / Cartailler, J.P. / Lanyi, J.K. #1: ![]() Title: Structure of Bacteriorhodopsin at 1.55 Angstrom Resolution Authors: Luecke, H. / Schobert, B. / Richter, H.-T. / Cartailler, J.-P. / Lanyi, J.K. #2: ![]() Title: Proton Transfer Pathways in Bacteriorhodopsin at 2.3 Angstrom Resolution Authors: Luecke, H. / Richter, H.-T. / 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 | ![]() | 63.2 KB | Display | ![]() |
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PDB format | ![]() | 43.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 780.7 KB | Display | ![]() |
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Full document | ![]() | 819.9 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1c8rC ![]() 1c3wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21369.309 Da / Num. of mol.: 1 / Mutation: D96N Source method: isolated from a genetically manipulated source Details: SCHIFF BASE LINKAGE BETWEEN LYS 216 (NZ) AND RET 301 (C15) DIETHER LIPID BILAYER Source: (gene. exp.) ![]() ![]() | ||||||
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#2: Chemical | ChemComp-LI1 / #3: Chemical | ChemComp-SQU / | #4: Chemical | ChemComp-RET / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.18 % | ||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: cubic lipid phase / pH: 5.6 Details: MO:WATER:PHOSPHATE, pH 5.6, CUBIC LIPID PHASE, temperature 296K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: other / Details: Gabriele, R., (1998) J. Struct. Biol., 121, 82. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2→25 Å / Num. obs: 14622 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.2 | |||||||||||||||
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.1 / % possible all: 98.1 | |||||||||||||||
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 25 Å / Num. measured all: 110517 | |||||||||||||||
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.33 |
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Processing
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Refinement | Method to determine structure: ISOMORPHOUS Starting model: PDB ENTRY 1C3W Resolution: 2→12 Å / Num. parameters: 7288 / Num. restraintsaints: 7357 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: MEROHEDRAL TWINNING RATIO OF 53:47
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Solvent computation | Solvent model: SHELXL-97 SWAT, BABINET'S PRINCIPLE | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→12 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.172 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |