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Yorodumi- PDB-5g2c: The crystal structure of light-driven chloride pump ClR (T102D) m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g2c | ||||||
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Title | The crystal structure of light-driven chloride pump ClR (T102D) mutant at pH 4.5. | ||||||
Components | CHLORIDE PUMPING RHODOPSIN | ||||||
Keywords | TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | NONLABENS MARINUS S1-08 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Kim, K.L. / Kwon, S.K. / Jun, S.H. / Cha, J.S. / Kim, H.Y. / Kim, J.H. / Cho, H.S. | ||||||
Citation | Journal: Nat.Commun. / Year: 2016 Title: Crystal Structure and Functional Characterization of a Light-Driven Chloride Pump Having an Ntq Motif. Authors: Kim, K. / Kwon, S. / Jun, S. / Cha, J.S. / Kim, H. / Lee, W. / Kim, J.F. / Cho, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g2c.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g2c.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 5g2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g2c_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5g2c_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5g2c_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 5g2c_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/5g2c ftp://data.pdbj.org/pub/pdb/validation_reports/g2/5g2c | HTTPS FTP |
-Related structure data
Related structure data | 5g28C 5g2aC 5g2dC 5g54C 3x3bS 5g29 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: 30503.746 Da / Num. of mol.: 1 / Fragment: SEVEN TRANS-MEMBRANE / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) NONLABENS MARINUS S1-08 (bacteria) / Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W8VZW3 |
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-Non-polymers , 5 types, 26 molecules
#2: Chemical | ChemComp-OLA / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-RET / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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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: 2.47 Å3/Da / Density % sol: 50.25 % / Description: NONE |
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Crystal grow | pH: 4.5 / Details: pH 4.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 13298 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.42 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.83 / % possible all: 73.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3X3B Resolution: 2.31→58.28 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.089 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.713 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→58.28 Å
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Refine LS restraints |
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