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- PDB-5kkh: 2.1-Angstrom In situ Mylar structure of bacteriorhodopsin from Ha... -
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Open data
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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 | |||||||||
![]() | Bacteriorhodopsin-I | |||||||||
![]() | MEMBRANE PROTEIN / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() photoreceptor activity / phototransduction / proton transmembrane transport / monoatomic ion channel activity / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Broecker, J. / Ernst, O.P. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.9 KB | Display | ![]() |
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PDB format | ![]() | 120.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5kkiC ![]() 5kkjC ![]() 5kkkC ![]() 2ei4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() Strain: DSM 16790 / HBSQ001 / Gene: bop1, bopI, HQ_1014A / Production host: ![]() ![]() #2: Chemical | ChemComp-OLC / ( #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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