+Open data
-Basic information
Entry | Database: PDB / ID: 4qid | ||||||
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Title | Crystal structure of Haloquadratum walsbyi bacteriorhodopsin | ||||||
Components | Bacteriorhodopsin-I | ||||||
Keywords | MEMBRANE PROTEIN / Bacteriorhodopsin / proton pump / membrane | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | ||||||
Biological species | Haloquadratum walsbyi (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | ||||||
Authors | Wang, A.H.J. / Hsu, M.F. / Yang, C.S. / Fu, H.Y. | ||||||
Citation | Journal: To be Published Title: An acid-tolerant light-driven proton pump Authors: Wang, A.H.J. / Hsu, M.F. / Yang, C.S. / Fu, H.Y. / Cai, C.J. / Yi, H.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qid.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qid.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 4qid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/4qid ftp://data.pdbj.org/pub/pdb/validation_reports/qi/4qid | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 28490.088 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haloquadratum walsbyi (archaea) / Strain: DSM 16790 / HBSQ001 / Gene: bop1, bopI, HQ_1014A / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: Q18DH8 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MPG / [( | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.92 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 4 Details: ammonium sulfate, NaCl, sodium acetate, PEG 200, pH 4.0, LIPID CUBIC PHASE, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 20, 2013 |
Radiation | Monochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→30 Å / Num. obs: 48309 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.168 / Rsym value: 0.168 / Net I/σ(I): 8.212 |
Reflection shell | Resolution: 2.58→2.67 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.016 / Rsym value: 0.791 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→28.87 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.435 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.717 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.988 Å2
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Refinement step | Cycle: LAST / Resolution: 2.57→28.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.568→2.635 Å / Total num. of bins used: 20
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