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Yorodumi- PDB-7ug8: Crystal structure of a solute receptor from Synechococcus CC9311 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ug8 | |||||||||
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Title | Crystal structure of a solute receptor from Synechococcus CC9311 in complex with alpha-ketovaleric and calcium | |||||||||
Components | Ketoacid-binding protein | |||||||||
Keywords | TRANSPORT PROTEIN / Substrate-binding protein / marine cyanobacteria / ketoacid-binding protein | |||||||||
Function / homology | Function and homology information organic acid transport / tripartite ATP-independent periplasmic transporter complex / organic acid binding / transmembrane transport / periplasmic space / metal ion binding Similarity search - Function | |||||||||
Biological species | Synechococcus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.796 Å | |||||||||
Authors | Shah, B.S. / Mikolajek, H. / Orr, C.M. / Mykhaylyk, V. / Owens, R.J. / Paulsen, I.T. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: To Be Published Title: Crystal structure of a solute receptor from Synechococcus CC9311 in complex with alpha-ketovaleric and calcium Authors: Shah, B.S. / Mikolajek, H. / Orr, C.M. / Mykhaylyk, V. / Owens, R. / Paulsen, I.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ug8.cif.gz | 264.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ug8.ent.gz | 209.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ug8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ug8_validation.pdf.gz | 491 KB | Display | wwPDB validaton report |
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Full document | 7ug8_full_validation.pdf.gz | 496.9 KB | Display | |
Data in XML | 7ug8_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 7ug8_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/7ug8 ftp://data.pdbj.org/pub/pdb/validation_reports/ug/7ug8 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 7 - 334 / Label seq-ID: 7 - 334
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
#1: Protein | Mass: 38460.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. (strain CC9311) (bacteria) Strain: CC9311 / Gene: sync_2776 / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo 21 (DE3) / References: UniProt: Q0I6F8 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.05 Å3/Da / Density % sol: 39.99 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.02 M Sodium/Potassium Phosphate, 0.1M Bis Tris propane 7.5, 20% Peg 3350 Cryo: 30 % Peg 400 |
-Data collection
Diffraction | Mean temperature: 50 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552, 3.1790, 3.4925, 4.7686 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Dec 12, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Entry-ID: 7UG8
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Reflection shell | Resolution: 9.06→50.23 Å / Redundancy: 23.3 % / Rmerge(I) obs: 0.039 / Num. unique obs: 451 / CC1/2: 0.999 / Rpim(I) all: 0.012 / Rrim(I) all: 0.041 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.796→50.277 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.728 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.121 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.394 Å2
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Refinement step | Cycle: LAST / Resolution: 1.796→50.277 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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