+Open data
-Basic information
Entry | Database: PDB / ID: 1iw6 | |||||||||
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Title | Crystal Structure of the Ground State of Bacteriorhodopsin | |||||||||
Components | bacteriorhodopsin | |||||||||
Keywords | PROTON TRANSPORT / 7 Helix / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | |||||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | |||||||||
Biological species | Halobacterium salinarum (Halophile) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Kouyama, T. / Okumura, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iw6.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iw6.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 1iw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/1iw6 ftp://data.pdbj.org/pub/pdb/validation_reports/iw/1iw6 | HTTPS FTP |
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-Related structure data
Related structure data | 1ixfC 1qm8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-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 |
-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) Halobacterium salinarum (Halophile) / Strain: jw3 / References: UniProt: P02945 |
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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
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 4, 2001 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→28.4 Å / Num. all: 16008 / Num. obs: 15703 / % possible obs: 99.7 % / Redundancy: 11.6 % / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2258 / Rsym value: 0.487 / % possible all: 99.7 |
Reflection | *PLUS Highest resolution: 2.3 Å |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.0477 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1qm8 Resolution: 2.3→28.4 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 56.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→28.4 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.248 | ||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.344 / Rfactor Rwork: 0.315 |