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Yorodumi- PDB-5ax1: Crystal Structure of the Cell-Free Synthesized Membrane Protein, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ax1 | |||||||||
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Title | Crystal Structure of the Cell-Free Synthesized Membrane Protein, Acetabularia Rhodopsin I, at 1.80 angstrom | |||||||||
Components | Rhodopsin I | |||||||||
Keywords | PROTON TRANSPORT / MEMBRANE PROTEIN / RETINAL / WATER CLUSTER / GREEN ALGAE / PHOTOTAXIS / CELL-FREE SYNTHESIS / MICROBIAL-TYPE RHODOPSIN / LIGHT-DRIVEN PROTON PUMP | |||||||||
Function / homology | Function and homology information phototransduction / photoreceptor activity / monoatomic ion channel activity / endoplasmic reticulum / plasma membrane Similarity search - Function | |||||||||
Biological species | Acetabularia acetabulum (mermaid's wine glass) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å | |||||||||
Authors | Furuse, M. / Hosaka, T. / Kimura-Someya, T. / Yokoyama, S. / Shirouzu, M. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum Authors: Furuse, M. / Tamogami, J. / Hosaka, T. / Kikukawa, T. / Shinya, N. / Hato, M. / Ohsawa, N. / Kim, S.Y. / Jung, K.H. / Demura, M. / Miyauchi, S. / Kamo, N. / Shimono, K. / Kimura-Someya, T. / ...Authors: Furuse, M. / Tamogami, J. / Hosaka, T. / Kikukawa, T. / Shinya, N. / Hato, M. / Ohsawa, N. / Kim, S.Y. / Jung, K.H. / Demura, M. / Miyauchi, S. / Kamo, N. / Shimono, K. / Kimura-Someya, T. / Yokoyama, S. / Shirouzu, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ax1.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ax1.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 5ax1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ax1_validation.pdf.gz | 686.5 KB | Display | wwPDB validaton report |
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Full document | 5ax1_full_validation.pdf.gz | 689.1 KB | Display | |
Data in XML | 5ax1_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 5ax1_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/5ax1 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/5ax1 | HTTPS FTP |
-Related structure data
Related structure data | 5awzC 5ax0C 1c3wS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26476.262 Da / Num. of mol.: 1 / Fragment: UNP residues 1-237 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetabularia acetabulum (mermaid's wine glass) Gene: aopI / Production host: Escherichia coli (E. coli) / References: UniProt: G3CEP6 |
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-Non-polymers , 7 types, 95 molecules
#2: Chemical | ChemComp-RET / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-C14 / | #5: Chemical | #6: Chemical | ChemComp-R16 / | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.04 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8 / Details: 20% PEG400, 0.1M Tris, 0.1M NaCl, 20mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX325HE / Detector: CCD / Date: Oct 31, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34.83 Å / Num. obs: 26610 / % possible obs: 99.54 % / Redundancy: 4.4 % / Biso Wilson estimate: 20.62 Å2 / Rsym value: 0.08568 / Net I/σ(I): 13.55 |
Reflection shell | Resolution: 1.8→1.87 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.91 / % possible all: 96.16 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C3W Resolution: 1.803→34.826 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.36 / 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: 1.803→34.826 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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