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Yorodumi- PDB-5ys3: 1.8 angstrom crystal structure of Succinate-Acetate Permease from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ys3 | ||||||||||||||||||
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Title | 1.8 angstrom crystal structure of Succinate-Acetate Permease from Citrobacter koseri | ||||||||||||||||||
Components | Succinate-Acetate Permease | ||||||||||||||||||
Keywords | TRANSPORT PROTEIN / organic anion channel / rectifying / unidirectional / dehydration | ||||||||||||||||||
Function / homology | Acetate transporter GPR1/FUN34/SatP family / GPR1/FUN34/yaaH family / GPR1/FUN34/yaaH family signature. / membrane / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / ACETATE ION / PALMITIC ACID / Acetate uptake transporter Function and homology information | ||||||||||||||||||
Biological species | Citrobacter koseri (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.823 Å | ||||||||||||||||||
Authors | Qiu, B. / Liao, J. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Cell Res. / Year: 2018 Title: Succinate-acetate permease from Citrobacter koseri is an anion channel that unidirectionally translocates acetate Authors: Qiu, B. / Xia, B. / Zhou, Q. / Lu, Y. / He, M. / Hasegawa, K. / Ma, Z. / Zhang, F. / Gu, L. / Mao, Q. / Wang, F. / Zhao, S. / Gao, Z. / Liao, J. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ys3.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ys3.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 5ys3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ys3_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 5ys3_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 5ys3_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 5ys3_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/5ys3 ftp://data.pdbj.org/pub/pdb/validation_reports/ys/5ys3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20473.240 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) (bacteria) Strain: ATCC BAA-895 / CDC 4225-83 / SGSC4696 / Gene: CKO_03375 / Production host: Escherichia coli (E. coli) / References: UniProt: A8ALU5 #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-PLM / #4: Chemical | ChemComp-78M / ( #5: Water | ChemComp-HOH / | |
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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: 2.39 Å3/Da / Density % sol: 48.52 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / pH: 6.5 / Details: PEG 400, CaAc2, NaCl / PH range: 4.0-6.5 / Temp details: PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 51162 / % possible obs: 99.6 % / Redundancy: 6.9 % / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.7 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.823→39.728 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.37 / 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: 1.823→39.728 Å
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Refine LS restraints |
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LS refinement shell |
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