+Open data
-Basic information
Entry | Database: PDB / ID: 2wjl | ||||||
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Title | Bacteriorhodopsin mutant E194D | ||||||
Components | Bacteriorhodopsin | ||||||
Keywords | PROTON TRANSPORT / ION PUMP / RETINAL PROTEIN / PHOTORECEPTOR PROTEIN / HYDROGEN ION TRANSPORT / PYRROLIDONE / MEROHEDRAL TWINNING / SENSORY TRANSDUCTION / SERPENTINE / CHROMOPHORE / PHOTORECEPTOR | ||||||
Function / homology | Function and homology information 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: 2.15 Å | ||||||
Authors | Potschies, M. / Wolf, S. / Freier, E. / Hofmann, E. / Gerwert, K. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2010 Title: Directional proton transfer in membrane proteins achieved through protonated protein-bound water molecules: a proton diode. Authors: Wolf, S. / Freier, E. / Potschies, M. / Hofmann, E. / Gerwert, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wjl.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wjl.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/2wjl ftp://data.pdbj.org/pub/pdb/validation_reports/wj/2wjl | HTTPS FTP |
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-Related structure data
Related structure data | 2wjkC 1c3wS 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
#1: Protein | Mass: 26915.475 Da / Num. of mol.: 1 / Mutation: E194D Source method: isolated from a genetically manipulated source Details: RETINAL LINKED VIA SCHIFF BASE TO K216 / Source: (gene. exp.) Halobacterium salinarum (Halophile) / Gene: bop, VNG_1467G / Production host: Halobacterium salinarum (Halophile) / References: UniProt: P02945 |
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#2: Chemical | ChemComp-RET / |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.1 % / Description: NONE |
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Crystal grow | Method: lipidic cubic phase / pH: 5.6 / Details: LIPID CUBIC PHASE AFTER LUECKE ET AL., pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98407 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98407 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 12843 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.2965 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.18 |
Reflection shell | Resolution: 2.15→2.3 Å / Redundancy: 6.16502 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.97 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C3W Resolution: 2.15→40 Å / Num. parameters: 7072 / Num. restraintsaints: 8545 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1756 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→40 Å
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Refine LS restraints |
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