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Yorodumi- PDB-1dze: Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dze | |||||||||
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Title | Structure of the M Intermediate of Bacteriorhodopsin trapped at 100K | |||||||||
Components | BACTERIORHODOPSIN (M INTERMEDIATE) | |||||||||
Keywords | BACTERIORHODOPSIN / PROTON PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / PHOTORECEPTOR / REACTION INTERMEDIATE / HALOBACTERIA / ION PUMP / HELIX / SLIDING | |||||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | |||||||||
Biological species | HALOBACTERIUM SALINARIUM (Halophile) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Takeda, K. / Matsui, Y. / Sato, H. / Hino, T. / Kanamori, E. / Okumura, H. / Yamane, T. / Iizuka, T. / Kamiya, N. / Adachi, S. / Kouyama, T. | |||||||||
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: Acta Crystallogr.,Sect.D / Year: 1999 Title: Specific Lipid-Protein Interactions in a Novel Honeycomb Lattice Structure of Bacteriorhodopsin Authors: Sato, H. / Takeda, K. / Tani, K. / Hino, T. / Okada, T. / Nakasako, M. / Kamiya, N. / Kouyama, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dze.cif.gz | 70.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dze.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/1dze ftp://data.pdbj.org/pub/pdb/validation_reports/dz/1dze | HTTPS FTP |
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-Related structure data
Related structure data | 1iw9C 1qm8S S: Starting model for refinement C: citing same article (ref.) |
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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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-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 / Details: HALOBACTERIUM SALINARIUM / Source: (natural) HALOBACTERIUM SALINARIUM (Halophile) / Cellular location: CELL MEMBRANE / 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 , 6 types, 24 molecules
#3: Chemical | ChemComp-RET / | ||||||
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#4: Chemical | ChemComp-L1P / | ||||||
#5: Chemical | #6: Chemical | ChemComp-L3P / | #7: Chemical | ChemComp-L4P / | #8: 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: 3.17 Å3/Da / Density % sol: 61.19 % Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD |
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Crystal grow | Method: vapor diffusion / pH: 5.2 Details: THE CRYSTALLIZATION CONSISTS OF TWO STEPS. FIRST, A MIXTURE OF 5 MG/ML PURPLE MEMBRANE, 0.25% OTG, 1 M AMMONIUM SULFATE, 0.16 M NACL, 0.04 M SODIUM CITRATE (PH5.2) , 0.04% NAN3 WAS INCUBATED ...Details: THE CRYSTALLIZATION CONSISTS OF TWO STEPS. FIRST, A MIXTURE OF 5 MG/ML PURPLE MEMBRANE, 0.25% OTG, 1 M AMMONIUM SULFATE, 0.16 M NACL, 0.04 M SODIUM CITRATE (PH5.2) , 0.04% NAN3 WAS INCUBATED AND 15% TREHALOSE AT 305K FOR 5 DAYS. THIS RESULTED IN THE FORMATION OF SPHERICAL VESICLES WITH A DIAMETER OF 50 NM. AFTER SEDIMENTAL MATERIALS WERE REMOVED BY CENTRIFUGATION (4000G X 10 MIN), A SUSPENSION OF THE SPHERICAL VESICLES WAS COOLED TO 278K AND CONCENTRATED BY VAPOR DIFFUSION AGAINST A RESERVOIR SOLUTION CONTAINING 2.0 M AMMONIUM SULFATE 0.08M SODIUM CITRATE (PH 5.2) AND 30% TREHALOSE. INCUBATION FOR A COUPLE OF MONTHS YIELDED HEXAGONAL CRYSTALS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 18, 1998 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 11480 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Rsym value: 0.069 |
Reflection shell | Resolution: 2.5→2.59 Å / Rsym value: 0.304 / % possible all: 55.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QM8 Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE C-TERMINAL RESIDUES WERE NOT SEEN IN THE DENSITY MAPS
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Displacement parameters | Biso mean: 36 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
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Xplor file |
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