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Yorodumi- PDB-5a44: Structure of Bacteriorhodopsin obtained from 20um crystals by mul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5a44 | ||||||
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Title | Structure of Bacteriorhodopsin obtained from 20um crystals by multi crystal data collection | ||||||
Components | BACTERIORHODOPSIN | ||||||
Keywords | PROTON TRANSPORT / MULTI CRYSTAL DATA COLLECTION / SYNCHROTRON SERIAL CRYSTALLOGRAPHY / LCP / SSX / ION PUMP / MEMBRANE PROTEIN / RETINAL PROTEIN / PHOTORECEPTOR / 7-HELIX TRANSMEMBRANE / ION TRANSPORT / MEMBRANE | ||||||
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 / OTHER / Resolution: 2.29 Å | ||||||
Authors | Zander, U. / Bourenkov, G. / Popov, A.N. / de Sanctis, D. / McCarthy, A.A. / Svensson, O. / Round, E.S. / Gordeliy, V.I. / Mueller-Dieckmann, C. / Leonard, G.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Meshandcollect: An Automated Multi-Crystal Data-Collection Workflow for Synchrotron Macromolecular Crystallography Beamlines. Authors: Zander, U. / Bourenkov, G. / Popov, A.N. / De Sanctis, D. / Svensson, O. / Mccarthy, A.A. / Round, E. / Gordeliy, V. / Mueller-Dieckmann, C. / Leonard, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a44.cif.gz | 54.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a44.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 5a44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/5a44 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/5a44 | HTTPS FTP |
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-Related 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: 26814.412 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 14-261 / Source method: isolated from a natural source / Source: (natural) HALOBACTERIUM SALINARUM (Halophile) / References: UniProt: P02945 | ||||
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#2: Chemical | ChemComp-RET / | ||||
#3: Chemical | ChemComp-LI1 / #4: Chemical | ChemComp-HP6 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→20.05 Å / Num. obs: 9802 / % possible obs: 92.7 % / Observed criterion σ(I): 2.7 / Redundancy: 4.8 % / Rmerge(I) obs: 0.03 |
-Processing
Software | Name: REFMAC / Version: 5.8.0103 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.29→20.01 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.779 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.438 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→20.01 Å
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Refine LS restraints |
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