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Yorodumi- PDB-6k6i: The crystal structure of light-driven cyanobacterial chloride imp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k6i | |||||||||
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Title | The crystal structure of light-driven cyanobacterial chloride importer from Mastigocladopsis repens | |||||||||
Components | Cyanobacterial chloride importer | |||||||||
Keywords | MEMBRANE PROTEIN / chloride ion pump / rhodopsin | |||||||||
Function / homology | Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha / OLEIC ACID / RETINAL Function and homology information | |||||||||
Biological species | Mastigocladopsis repens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Yun, J.H. / Park, J.H. / Jin, Z. / Ohki, M. / Wang, Y. / Lupala, C.S. / Kim, M. / Liu, H. / Park, S.Y. / Lee, W. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: To Be Published Title: The crystal structure of light-driven cyanobacterial chloride importer from Mastigocladopsis repens Authors: Yun, J.H. / Park, J.H. / Jin, Z. / Ohki, M. / Wang, Y. / Lupala, C.S. / Kim, M. / Liu, H. / Park, S.Y. / Lee, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k6i.cif.gz | 65.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k6i.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 6k6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/6k6i ftp://data.pdbj.org/pub/pdb/validation_reports/k6/6k6i | HTTPS FTP |
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-Related structure data
Related structure data | 5itcS 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: 26060.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mastigocladopsis repens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) | ||||||
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#2: Chemical | ChemComp-RET / | ||||||
#3: Chemical | ChemComp-OLA / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.46 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 4.9 / Details: Magnesium nitrate hexahydrate, Sodium citrate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20.2 Å / Num. obs: 21720 / % possible obs: 96.1 % / Redundancy: 6.1 % / Biso Wilson estimate: 22.4 Å2 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 997 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ITC Resolution: 1.9→20.2 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.152 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.154 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.138
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Displacement parameters | Biso mean: 33.19 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→20.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.91 Å / Total num. of bins used: 50
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