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- PDB-5ahz: Bromide-bound form of Halorhodopsin from Halobacterium salinarum ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ahz | ||||||
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Title | Bromide-bound form of Halorhodopsin from Halobacterium salinarum in a new rhombohedral crystal form | ||||||
![]() | HALORHODOPSIN | ||||||
![]() | MEMBRANE PROTEIN / TRANSPORT PROTEIN / HALOPHILIC ARCHAEA / ARCHAEAL RHODOPSIN / LIGHT DRIVEN ION PUMP / RETINAL PROTEIN / ION TRANSMEMBRANE TRANSPORT | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schreiner, M. / Schlesinger, R. / Heberle, J. / Niemann, H.H. | ||||||
![]() | ![]() Title: Structure of Halorhodopsin from Halobacterium Salinarum in a New Crystal Form that Imposes Little Restraint on the E-F Loop. Authors: Schreiner, M. / Schlesinger, R. / Heberle, J. / Niemann, H.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.6 KB | Display | ![]() |
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PDB format | ![]() | 43.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 841.7 KB | Display | ![]() |
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Full document | ![]() | 844.5 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ahySC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-RET / | ||||||||
#3: Chemical | #4: Sugar | ChemComp-BOG / | #5: Water | ChemComp-HOH / | Nonpolymer details | RETINAL (RET): RETINAL IS COVALENTLY | Sequence details | AMINO ACIDS 1-19 ARE MISSING (CLEAVED SIGNAL PEPTIDE), C- TERMINAL HEXAHISTID | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.82 % / Description: NONE |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion Details: RESERVOIR SOLUTION: 100 MM CITRATE PH 8, 150 MM NABR, 2.3 M (NH4)2SO4. VAPOR DIFFUSION AT 296 K WITH DROP RATIO OF 1.2 TO 0.8 UL PROTEIN TO RESERVOIR. PROTEIN CONCENTRATION 7 MG/ML. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2013 / Details: PT COATED SI MIRROR |
Radiation | Monochromator: CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→42.8 Å / Num. obs: 10814 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 40.53 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.98 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: ISOMORPHOUS STRUCTURE OF CHLORIDE-BOUND HALORHODOPSIN, PDB ID 5AHY Resolution: 2.45→42.836 Å / SU ML: 0.32 / σ(F): 1.35 / Phase error: 26.8 / Stereochemistry target values: ML Details: RESIDUES 263-274 AS WELL AS THE C-TERMINAL HEXAHISTIDINE-TAG ARE 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: 41.1 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→42.836 Å
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Refine LS restraints |
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LS refinement shell |
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