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Yorodumi- PDB-5xar: Structural insights into the elevator-like mechanism of the sodiu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xar | ||||||||||||
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Title | Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS | ||||||||||||
Components | Citrate-sodium symporter | ||||||||||||
Keywords | TRANSPORT PROTEIN / CitS / citrate transporter / sodium/citrate symporter / 2-HCT | ||||||||||||
Function / homology | 2-hydroxycarboxylate transporter / 2-hydroxycarboxylate transporter, Proteobacteria/Firmicutes / 2-hydroxycarboxylate transporter family / citrate metabolic process / organic anion transmembrane transporter activity / symporter activity / plasma membrane / Citrate-sodium symporter Function and homology information | ||||||||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 Å | ||||||||||||
Authors | Jin, M.S. / Kim, J.W. / Kim, S. / Kim, S. / Lee, H. / Lee, J.-O. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: Sci Rep / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xar.cif.gz | 642.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xar.ent.gz | 537.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xar_validation.pdf.gz | 787.8 KB | Display | wwPDB validaton report |
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Full document | 5xar_full_validation.pdf.gz | 823.9 KB | Display | |
Data in XML | 5xar_validation.xml.gz | 59 KB | Display | |
Data in CIF | 5xar_validation.cif.gz | 80.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/5xar ftp://data.pdbj.org/pub/pdb/validation_reports/xa/5xar | HTTPS FTP |
-Related structure data
Related structure data | 5x9rC 5xasC 5xatC 5a1sS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 46673.430 Da / Num. of mol.: 4 / Fragment: UNP residues 13-446 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: citS / Production host: Bacteria (eubacteria) / References: UniProt: P31602 #2: Chemical | ChemComp-NA / #3: Sugar | #4: Water | ChemComp-HOH / | Sequence details | Author replaced the 7-PPATEK-12 amino acid region of KpCitS with a thrombin recognition sequence (LVPRGS) | |
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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: 3.44 Å3/Da / Density % sol: 68.25 % |
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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 PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jul 19, 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: 3.6→93.49 Å / Num. obs: 30477 / % possible obs: 99.6 % / Redundancy: 3.7 % / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 3.6→3.7 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5A1S Resolution: 3.62→93.49 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.931 / SU B: 106.757 / SU ML: 0.623 / Cross valid method: THROUGHOUT / ESU R Free: 0.647 / 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: 189.555 Å2
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Refinement step | Cycle: 1 / Resolution: 3.62→93.49 Å
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Refine LS restraints |
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