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- PDB-5x9r: Structural insights into the elevator-like mechanism of the sodiu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5x9r | ||||||||||||
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Title | Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS | ||||||||||||
![]() | Citrate-sodium symporter | ||||||||||||
![]() | TRANSPORT PROTEIN / CitS / citrate transporter / sodium/citrate symporter / 2-HCT | ||||||||||||
Function / homology | ![]() citrate metabolic process / organic anion transmembrane transporter activity / symporter activity / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Jin, M.S. / Kim, J.W. / Kim, S. / Kim, S. / Lee, H. / Lee, J.-O. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS Authors: Kim, J.W. / Kim, S. / Kim, S. / Lee, H. / Lee, J.O. / Jin, M.S. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332.3 KB | Display | ![]() |
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PDB format | ![]() | 276 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.5 KB | Display | ![]() |
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Full document | ![]() | 510.2 KB | Display | |
Data in XML | ![]() | 33 KB | Display | |
Data in CIF | ![]() | 43 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xarC ![]() 5xasC ![]() 5xatC ![]() 5a1sS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 21 - 444 / Label seq-ID: 11 - 434
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Components
#1: Protein | Mass: 46673.430 Da / Num. of mol.: 2 / Fragment: UNP residues 13-446 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #2: Chemical | #3: Sugar | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 71.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 100 mM MES pH 6.0-6.5, 100-200 mM NaCl, 32-36% PEG400, 5mM Sodium Citrate PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jun 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.98→94 Å / Num. obs: 12743 / % possible obs: 99.2 % / Redundancy: 6.8 % / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 4→4.1 Å / % possible obs: 99.9 % / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A1S Resolution: 3.98→94 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.898 / SU B: 143.199 / SU ML: 0.785 / Cross valid method: THROUGHOUT / ESU R Free: 0.941 / 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: 269.517 Å2
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Refinement step | Cycle: 1 / Resolution: 3.98→94 Å
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Refine LS restraints |
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