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Yorodumi- PDB-5kkh: 2.1-Angstrom In situ Mylar structure of bacteriorhodopsin from Ha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kkh | |||||||||
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Title | 2.1-Angstrom In situ Mylar structure of bacteriorhodopsin from Haloquadratum walsbyi (HwBR) at 100 K | |||||||||
Components | Bacteriorhodopsin-I | |||||||||
Keywords | MEMBRANE PROTEIN / TRANSPORT PROTEIN | |||||||||
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: 2.125 Å | |||||||||
Authors | Broecker, J. / Ernst, O.P. | |||||||||
Funding support | Canada, Germany, 2items
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Citation | Journal: Cryst Growth Des / Year: 2016 Title: A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals. Authors: Broecker, J. / Klingel, V. / Ou, W.L. / Balo, A.R. / Kissick, D.J. / Ogata, C.M. / Kuo, A. / Ernst, O.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kkh.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kkh.ent.gz | 120.7 KB | Display | PDB format |
PDBx/mmJSON format | 5kkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/5kkh ftp://data.pdbj.org/pub/pdb/validation_reports/kk/5kkh | HTTPS FTP |
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-Related structure data
Related structure data | 5kkiC 5kkjC 5kkkC 2ei4S C: citing same article (ref.) 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
#1: Protein | Mass: 29116.809 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haloquadratum walsbyi (strain DSM 16790 / HBSQ001) (archaea) Strain: DSM 16790 / HBSQ001 / Gene: bop1, bopI, HQ_1014A / Production host: Escherichia coli (E. coli) / References: UniProt: Q18DH8 #2: Chemical | ChemComp-OLC / ( #3: Chemical | #4: Chemical | #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: 1.97 Å3/Da / Density % sol: 37.7 % / Description: small compact, hexagonal plates |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7 / Details: 8% (v/v) Tacsimate, 20% (v/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.125→29.45 Å / Num. all: 57569 / Num. obs: 35323 / % possible obs: 91 % / Redundancy: 1.8 % / Biso Wilson estimate: 14.86 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.107 / Net I/σ(I): 6.26 |
Reflection shell | Resolution: 2.13→2.2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.66 / % possible all: 70 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EI4 Resolution: 2.125→29.446 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.125→29.446 Å
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Refine LS restraints |
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LS refinement shell |
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