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Yorodumi- PDB-7qoa: Structure of CodB, a cytosine transporter in an outward-facing co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qoa | ||||||
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Title | Structure of CodB, a cytosine transporter in an outward-facing conformation | ||||||
Components | Cytosine permease | ||||||
Keywords | TRANSPORT PROTEIN / Membrane Transporter / Cytosine / Sodium | ||||||
Function / homology | cytosine transmembrane transporter activity / Cytosine permease / Purine-cytosine permease / Permease for cytosine/purines, uracil, thiamine, allantoin / membrane => GO:0016020 / 2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 6-AMINOPYRIMIDIN-2(1H)-ONE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Cytosine permease Function and homology information | ||||||
Biological species | Proteus vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Hatton, C.E. / Cameron, A.D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Embo J. / Year: 2022 Title: Structure of cytosine transport protein CodB provides insight into nucleobase-cation symporter 1 mechanism. Authors: Hatton, C.E. / Brotherton, D.H. / Spencer, M. / Cameron, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qoa.cif.gz | 200.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qoa.ent.gz | 125.9 KB | Display | PDB format |
PDBx/mmJSON format | 7qoa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qoa_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 7qoa_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7qoa_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 7qoa_validation.cif.gz | 41.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/7qoa ftp://data.pdbj.org/pub/pdb/validation_reports/qo/7qoa | HTTPS FTP |
-Related structure data
Related structure data | 2jlnS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 44191.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: EKQ45_12260 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A857SHB2 #4: Sugar | ChemComp-LMT / | |
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-Non-polymers , 5 types, 76 molecules
#2: Chemical | #3: Chemical | ChemComp-PEF / | #5: Chemical | ChemComp-A6L / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.28 Å3/Da / Density % sol: 62.48 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6.5 Details: 0.1 M Sodium Cacodylate pH 6.5, 0.45 M NaCl, 39% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→73.16 Å / Num. obs: 45754 / % possible obs: 99.41 % / Redundancy: 12.7 % / Biso Wilson estimate: 42.05 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.3739 / Net I/σ(I): 11.57 |
Reflection shell | Resolution: 2.4→2.49 Å / Num. unique obs: 4436 / CC1/2: 0.466 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JLN Resolution: 2.4→73.16 Å / SU ML: 0.331 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1704 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→73.16 Å
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Refine LS restraints |
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LS refinement shell |
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