+Open data
-Basic information
Entry | Database: PDB / ID: 1iw9 | |||||||||
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Title | Crystal Structure of the M Intermediate of Bacteriorhodopsin | |||||||||
Components | bacteriorhodopsin | |||||||||
Keywords | PROTON TRANSPORT / 7 Transmembrane Helices / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | |||||||||
Function / homology | Function and homology information light-driven active monoatomic ion transmembrane transporter activity / 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: 2.5 Å | |||||||||
Authors | Takeda, K. / Matsui, Y. / Kamiya, N. / Adachi, S. / Okumura, H. / Kouyama, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 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: Journal: J.Mol.Biol. / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iw9.cif.gz | 68.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iw9.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 1iw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iw9_validation.pdf.gz | 651.2 KB | Display | wwPDB validaton report |
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Full document | 1iw9_full_validation.pdf.gz | 678.1 KB | Display | |
Data in XML | 1iw9_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 1iw9_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/1iw9 ftp://data.pdbj.org/pub/pdb/validation_reports/iw/1iw9 | HTTPS FTP |
-Related structure data
Related structure data | 1dzeSC 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, 31 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: 3 |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.708 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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