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- PDB-5g2d: The crystal structure of light-driven chloride pump ClR (T102N) m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5g2d | ||||||
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Title | The crystal structure of light-driven chloride pump ClR (T102N) mutant at pH 4.5. | ||||||
![]() | CHLORIDE PUMP RHODOPSIN | ||||||
![]() | TRANSPORT PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, K.L. / Kwon, S.K. / Jun, S.H. / Cha, J.S. / Kim, H.Y. / Kim, J.H. / Cho, H.S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.6 KB | Display | ![]() |
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PDB format | ![]() | 52 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g28C ![]() 5g2aC ![]() 5g2cC ![]() 5g54C ![]() 3x3bS ![]() 5g29 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30502.762 Da / Num. of mol.: 1 / Fragment: SEVEN TRANS-MEMBRANE / Mutation: YES [T102N] Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 105 molecules ![](data/chem/img/OLA.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/RET.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-OLA / #3: Chemical | ChemComp-RET / | #4: Chemical | ChemComp-PEG / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.64 % / 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: ![]() ![]() |
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: 1.75→1.78 Å / Num. obs: 27489 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.67 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / % possible all: 81.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3X3B Resolution: 1.8→58.36 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.834 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.115 / 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: 24.456 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→58.36 Å
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Refine LS restraints |
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