+Open data
-Basic information
Entry | Database: PDB / ID: 1ucq | |||||||||
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Title | Crystal structure of the L intermediate of bacteriorhodopsin | |||||||||
Components | bacteriorhodopsin | |||||||||
Keywords | PROTON TRANSPORT / proton pump / retinal protein / membrane protein / protein-lipid complex / reaction intermediate | |||||||||
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: 2.4 Å | |||||||||
Authors | Kouyama, T. / Nishikawa, T. / Tokuhisa, T. / Okumura, H. | |||||||||
Citation | 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 | 1ucq.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ucq.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ucq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/1ucq ftp://data.pdbj.org/pub/pdb/validation_reports/uc/1ucq | HTTPS FTP |
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-Related structure data
Related structure data | 1iw6S S: Starting model for refinement |
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Similar structure data |
-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: -y, x-y, z and -x+y, -x, z. |
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 26929.500 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: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.13 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: ammonium sulfate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 278.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ / 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: BL40B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2003 |
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: 2.4→50 Å / Num. all: 13880 / Num. obs: 13880 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 50.406 Å2 / Rsym value: 0.066 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 1986 / Rsym value: 0.492 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 30 Å / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 49.2 % / Num. measured obs: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1iw6 Resolution: 2.4→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Diffraction data were collected for a 4:1 mixture of the ground state and the L intermediate. For refinement of the L-state structure, the contribution of the ground state was subtracted ...Details: Diffraction data were collected for a 4:1 mixture of the ground state and the L intermediate. For refinement of the L-state structure, the contribution of the ground state was subtracted using diffraction data collected for the pure ground state.
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Displacement parameters | Biso mean: 66.4738 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50.3 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.332 / Rfactor Rwork: 0.3 | |||||||||||||||||||||
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 |