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Yorodumi- PDB-3am6: Crystal structure of the proton pumping rhodopsin AR2 from marine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3am6 | ||||||
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Title | Crystal structure of the proton pumping rhodopsin AR2 from marine alga Acetabularia acetabulum | ||||||
Components | rhodopsin-2 | ||||||
Keywords | TRANSPORT PROTEIN / seven trans-membrane | ||||||
Function / homology | Function and homology information : / photoreceptor activity / phototransduction / monoatomic ion channel activity / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Acetabularia acetabulum (mermaid's wine glass) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Wada, T. / Yokoyama, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Crystal structure of the eukaryotic light-driven proton-pumping rhodopsin, Acetabularia rhodopsin II, from marine alga Authors: Wada, T. / Shimono, K. / Kikukawa, T. / Hato, M. / Shinya, N. / Kim, S.Y. / Kimura-Someya, T. / Shirouzu, M. / Tamogami, J. / Miyauchi, S. / Jung, K.-H. / Kamo, N. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3am6.cif.gz | 179.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3am6.ent.gz | 153 KB | Display | PDB format |
PDBx/mmJSON format | 3am6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/3am6 ftp://data.pdbj.org/pub/pdb/validation_reports/am/3am6 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 25563.168 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetabularia acetabulum (mermaid's wine glass) Plasmid: pCR2.1-TOPO / Production host: cell-free synthesis (others) / References: UniProt: G1K3Q0*PLUS #2: Chemical | ChemComp-RET / #3: Chemical | ChemComp-CLR / Sequence details | THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEINS AT THE TIME OF PROCESSING. THE ...THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEINS AT THE TIME OF PROCESSING | |
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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: 2.93 Å3/Da / Density % sol: 58.08 % |
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Crystal grow | Temperature: 293 K / Method: lipid mesophase / pH: 7.5 Details: 0.1M Tris-HCl (pH 7.5), 6% 2-methyl-2,4-pentanediol, 14% polyethylene glycol 400, lipid mesophase, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2009 |
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: 3.192→50 Å / Num. obs: 18284 / % possible obs: 89.5 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.115 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.192→3.31 Å / Redundancy: 2.5 % / Rsym value: 0.251 / % possible all: 72.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→36.2 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.837 / Rfactor Rfree error: 0.011 / SU B: 28.947 / SU ML: 0.505 / Data cutoff high absF: 53692.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.697 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.9644 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→36.2 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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