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Open data
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Basic information
Entry | Database: PDB / ID: 1iw9 | |||||||||
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Title | Crystal Structure of the M Intermediate of Bacteriorhodopsin | |||||||||
![]() | bacteriorhodopsin | |||||||||
![]() | PROTON TRANSPORT / 7 Transmembrane Helices / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | |||||||||
Function / homology | ![]() photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Takeda, K. / Matsui, Y. / Kamiya, N. / Adachi, S. / Okumura, H. / Kouyama, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
![]() | ![]() Title: Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix Authors: Takeda, K. / Matsui, Y. / Kamiya, N. / Adachi, S. / Okumura, H. / Kouyama, T. #1: ![]() Title: Crystal Structure of the L Intermediate of Bacteriorhodopsin: Evidence for Vertical Translocation of a Water Molecule during the Proton Pumping Cycle Authors: Kouyama, T. / Nishikawa, T. / Tokuhisa, T. / Okumura, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.5 KB | Display | ![]() |
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PDB format | ![]() | 48.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 651.2 KB | Display | ![]() |
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Full document | ![]() | 678.1 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dzeSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations:1-y, x-y, z and 1-x+y, 1-x, z |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 26814.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Polysaccharide | beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 31 molecules ![](data/chem/img/RET.gif)
![](data/chem/img/L3P.gif)
![](data/chem/img/L2P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/L3P.gif)
![](data/chem/img/L2P.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-RET / | ||||
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#4: Chemical | ChemComp-L3P / #5: Chemical | ChemComp-L2P / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.11 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: ammonium sulfate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 18, 1998 / Details: mirrors |
Radiation | Monochromator: DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.708 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 12434 / Num. obs: 11480 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 2.5→2.59 Å / Rsym value: 0.304 / % possible all: 55.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 10066 / % possible obs: 92.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 92.1 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 1.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1dze Resolution: 2.5→15.3 Å / Isotropic thermal model: Overall / Cross valid method: troughout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 47 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→15.3 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement | *PLUS Lowest resolution: 28 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.236 | |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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