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Open data
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Basic information
Entry | Database: PDB / ID: 1ixf | |||||||||
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Title | Crystal Structure of the K intermediate of bacteriorhodopsin | |||||||||
![]() | bacteriorhodopsin | |||||||||
![]() | PROTON TRANSPORT / 7-helices / 13-cis retinal / 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 | ![]() ![]() ![]() | |||||||||
![]() | Matsui, Y. / Sakai, K. / Murakami, M. / Shiro, Y. / Adachi, S. / Okumura, H. / Kouyama, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
![]() | ![]() Title: Specific Damage Induced by X-ray Radiation and Structural Changes in the Primary Photoreaction of Bacteriorhodopsin Authors: Matsui, Y. / Sakai, K. / Murakami, M. / Shiro, Y. / Adachi, S. / Okumura, H. / 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 | ![]() | 68.6 KB | Display | ![]() |
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PDB format | ![]() | 48.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 654.8 KB | Display | ![]() |
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Full document | ![]() | 683.2 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 15.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iw6SC 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: -y, x-y, z and -x+y, -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, 47 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: 61.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: MACSCIENCE / Detector: CCD / Date: Dec 7, 2000 / 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: 2.6→30 Å / Num. all: 11141 / Num. obs: 11120 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 13.8 % / Biso Wilson estimate: 60.49 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1579 / Rsym value: 0.533 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 11141 / % possible obs: 99.9 % / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1iw6 Resolution: 2.6→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 60.489 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.285 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.506 / Rfactor Rwork: 0.503 |