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Yorodumi- PDB-1mgy: Structure of the D85S mutant of bacteriorhodopsin with bromide bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mgy | ||||||
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Title | Structure of the D85S mutant of bacteriorhodopsin with bromide bound | ||||||
Components | Bacteriorhodopsin | ||||||
Keywords | PROTON TRANSPORT / bacteriorhodopsin / anion / pump / bromide / halide | ||||||
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 Å | ||||||
Authors | Facciotti, M.T. / Cheung, V.S. / Nguyen, D. / Rouhani, S. / Glaeser, R.M. | ||||||
Citation | Journal: Biophys.J. / Year: 2003 Title: Crystal Structure of the Bromide-Bound D85S Mutant of Bacteriorhodopsin: Principles of Ion Pumping Authors: Facciotti, M.T. / Cheung, V.S. / Nguyen, D. / Rouhani, S. / Glaeser, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mgy.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mgy.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mgy_validation.pdf.gz | 532.1 KB | Display | wwPDB validaton report |
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Full document | 1mgy_full_validation.pdf.gz | 535.5 KB | Display | |
Data in XML | 1mgy_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 1mgy_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/1mgy ftp://data.pdbj.org/pub/pdb/validation_reports/mg/1mgy | HTTPS FTP |
-Related structure data
Related structure data | 1kgbS 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26901.490 Da / Num. of mol.: 1 / Mutation: D85S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halobacterium salinarum (Halophile) / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945 |
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-Non-polymers , 5 types, 59 molecules
#2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-RET / | #5: Chemical | ChemComp-LI1 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.72 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: connected bilayer gel / pH: 4.6 Details: Sodium Acetate, PEG 4000, potassium chloride, mono-olein, pH 4.6, connected bilayer gel, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||||||||||||
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: ALS / Beamline: 8.3.1 / Wavelength: 1.1272 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 7, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 2→60 Å / Num. all: 16336 / Num. obs: 16336 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 89.8 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 135550 / Rmerge(I) obs: 0.127 |
Reflection shell | *PLUS % possible obs: 89.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1KGB Resolution: 2→12 Å / σ(F): 0
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→12 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Lowest resolution: 12 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2365 / Rfactor Rwork: 0.2151 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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