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- PDB-5da4: Structure of a nanobody recognizing the fumarate transporter SLC26Dg -
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Open data
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Basic information
Entry | Database: PDB / ID: 5da4 | |||||||||
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Title | Structure of a nanobody recognizing the fumarate transporter SLC26Dg | |||||||||
![]() | Nanobody recognizing the membrane protein SLC26Dg | |||||||||
![]() | IMMUNE SYSTEM / Membrane transport protein / nanobody complex | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dutzler, R. / Geertsma, E.R. / Chang, Y. / Shaik, F.R. | |||||||||
![]() | ![]() Title: Structure of a prokaryotic fumarate transporter reveals the architecture of the SLC26 family. Authors: Geertsma, E.R. / Chang, Y.N. / Shaik, F.R. / Neldner, Y. / Pardon, E. / Steyaert, J. / Dutzler, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.4 KB | Display | ![]() |
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PDB format | ![]() | 66.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.6 KB | Display | ![]() |
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Full document | ![]() | 431.2 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5da0C ![]() 5iofC ![]() 4wgv S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 13304.595 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Hepes pH 7.5, 200 mM CaCl2, 28% PEG400 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 76545 / % possible obs: 99.9 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 14.7 % / Rmerge(I) obs: 1.357 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WGV ![]() 4wgv Resolution: 2.4→19.996 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.44 / 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: 2.4→19.996 Å
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Refine LS restraints |
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LS refinement shell |
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