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Yorodumi- PDB-6a6n: Crystal structure of an inward-open apo state of the eukaryotic A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a6n | ||||||
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Title | Crystal structure of an inward-open apo state of the eukaryotic ABC multidrug transporter CmABCB1 | ||||||
Components | ATP-binding cassette, sub-family B, member 1ATP-binding cassette transporter | ||||||
Keywords | TRANSPORT PROTEIN / ALPHA-HELICAL | ||||||
Function / homology | Function and homology information ABC-type transporter activity / chloroplast / ATP hydrolysis activity / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Cyanidioschyzon merolae strain 10D (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å | ||||||
Authors | Kato, H. / Nakatsu, T. / Kodan, A. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Inward- and outward-facing X-ray crystal structures of homodimeric P-glycoprotein CmABCB1. Authors: Kodan, A. / Yamaguchi, T. / Nakatsu, T. / Matsuoka, K. / Kimura, Y. / Ueda, K. / Kato, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a6n.cif.gz | 129.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a6n.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 6a6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/6a6n ftp://data.pdbj.org/pub/pdb/validation_reports/a6/6a6n | HTTPS FTP |
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-Related structure data
Related structure data | 6a6mC 3wmeS S: Starting model for refinement C: citing same article (ref.) |
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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: 66046.609 Da / Num. of mol.: 1 / Mutation: Q147A, T381A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanidioschyzon merolae strain 10D (eukaryote) Strain: 10D / Gene: CYME_CMD148C / Plasmid: pABC3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AD1-8u- / References: UniProt: M1VAN7 | ||||
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#2: Sugar | ChemComp-DMU / #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 14% PEG 2000 MME, 100mM magnesium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2014 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→47.14 Å / Num. obs: 19238 / % possible obs: 99.6 % / Redundancy: 9.98 % / Rsym value: 0.102 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 3.02→3.1 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WME Resolution: 3.02→47.14 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.839 / SU B: 22.948 / SU ML: 0.398 / Cross valid method: THROUGHOUT / ESU R: 7.819 / ESU R Free: 0.422 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.306 Å2
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Refinement step | Cycle: 1 / Resolution: 3.02→47.14 Å
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Refine LS restraints |
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