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Yorodumi- PDB-3wqj: Crystal structure of archaerhodopsin-2 at 1.8 angstrom resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wqj | ||||||
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Title | Crystal structure of archaerhodopsin-2 at 1.8 angstrom resolution | ||||||
Components | Archaerhodopsin-2 | ||||||
Keywords | TRANSPORT PROTEIN / 7 trans-membrane helices / light-driven proton pump | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | Halobacterium (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kouyama, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structure of archaerhodopsin-2 at 1.8 angstrom resolution. Authors: Kouyama, T. / Fujii, R. / Kanada, S. / Nakanishi, T. / Chan, S.K. / Murakami, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wqj.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wqj.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/3wqj ftp://data.pdbj.org/pub/pdb/validation_reports/wq/3wqj | HTTPS FTP |
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-Related structure data
Related structure data | 2ei4S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27953.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halobacterium (Halophile) / Strain: AUS-2 / References: UniProt: P29563 |
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-Non-polymers , 8 types, 59 molecules
#2: Chemical | ChemComp-RET / | ||||
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#3: Chemical | ChemComp-22B / | ||||
#4: Chemical | ChemComp-SO4 / | ||||
#5: Chemical | ChemComp-L2P / | ||||
#6: Chemical | ChemComp-L3P / | ||||
#7: Chemical | #8: Chemical | ChemComp-SQL / ( | #9: 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: 2.25 Å3/Da / Density % sol: 45.23 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.8M AMMONIUM SULFATE, 0.1M HEPES, 0.32% NONYLGLUCOSIDE, 8% trehalose, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2013 |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.11 Å / Num. all: 24035 / Num. obs: 21944 / % possible obs: 91.3 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 8.8 % / Biso Wilson estimate: 23.15 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5.1 / Num. unique all: 3460 / Rsym value: 0.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EI4 Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.996 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.68 Å2 / Biso mean: 26.661 Å2 / Biso min: 11.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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