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Yorodumi- PDB-5g36: Yellow form of Halorhodopsin from Halobacterium salinarum in a ne... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g36 | ||||||
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Title | Yellow form of Halorhodopsin from Halobacterium salinarum in a new rhombohedral crystal form | ||||||
Components | HALORHODOPSIN | ||||||
Keywords | MEMBRANE PROTEIN / TRANSPORT PROTEIN / HALOPHILIC ARCHAEA / ARCHAEAL RHODOPSIN / LIGHT DRIVEN ION PUMP / RETINAL PROTEIN / ION TRANSMEMBRANE TRANSPORT | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | HALOBACTERIUM SALINARUM (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.6 Å | ||||||
Authors | Schreiner, M. / Schlesinger, R. / Heberle, J. / Niemann, H.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Crystal Structure of Halobacterium Salinarum Halorhodopsin with Partially Depopulated Primary Chloride Binding Site Authors: Schreiner, M. / Schlesinger, R. / Heberle, J. / Niemann, H.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g36.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g36.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 5g36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/5g36 ftp://data.pdbj.org/pub/pdb/validation_reports/g3/5g36 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27945.709 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-274 Source method: isolated from a genetically manipulated source Details: IMINE BOND (SCHIFF BASE) BETWEEN NZ OF LYS242 AND C15 OF THE RETINAL LIGAND Source: (gene. exp.) HALOBACTERIUM SALINARUM (Halophile) / Strain: L33 / Production host: HALOBACTERIUM SALINARUM (Halophile) / Strain (production host): L33 / References: UniProt: B0R2U4 |
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#2: Chemical | ChemComp-RET / |
#3: Chemical | ChemComp-CL / |
#4: Sugar | ChemComp-BOG / |
#5: Water | ChemComp-HOH / |
Sequence details | AMINO ACIDS 1-19 ARE MISSING (CLEAVED SIGNAL PEPTIDE), C- TERMINAL HEXAHISTID |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.48 % Description: ISOMORPHOUS STRUCTURE OF CHLORIDE-BOUND HALORHODOPSIN, PDB ENTRY 5AHY |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion Details: RESERVOIR SOLUTION: 100 MM BICINE PH 8, 150 MM NACL, 2.4 M (NH4)2SO4. VAPOR DIFFUSION AT 296 K WITH DROP RATIO OF 1.2 TO 0.8 UL PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION: 4.9 MG/ML. POST- ...Details: RESERVOIR SOLUTION: 100 MM BICINE PH 8, 150 MM NACL, 2.4 M (NH4)2SO4. VAPOR DIFFUSION AT 296 K WITH DROP RATIO OF 1.2 TO 0.8 UL PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION: 4.9 MG/ML. POST-CRYSTALLIZATION SOAKING SOLUTION: 100 MM GLYCINE PH 10, 2.6 M (NH4)2SO4 PH 10, 25% SUCROSE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9202 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2013 / Details: BENDABLE MIRRORS |
Radiation | Monochromator: CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9202 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→45.5 Å / Num. obs: 8774 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 31.77 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.6→2.73 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.8 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.6→42.393 Å / σ(F): 1.34 / Stereochemistry target values: ML Details: THE WHOLE SECTION C-TERMINAL TO ALA261 IS DISORDERED
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→42.393 Å
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Refine LS restraints |
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LS refinement shell |
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