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Yorodumi- PDB-8q2o: Structure of alginate transporter AlgE from P. aeruginosa PAO1 by... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q2o | |||||||||
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Title | Structure of alginate transporter AlgE from P. aeruginosa PAO1 by using Se-MAG for the the lipid cubic phase crystallization | |||||||||
Components | Alginate production protein AlgE | |||||||||
Keywords | TRANSPORT PROTEIN / alginate transporter / co-crystallization / experimental phasing / seleno-monoacylglyceride / X-ray scattering | |||||||||
Function / homology | Alginate export domain / Alginate export / alginic acid biosynthetic process / cell outer membrane / CITRATE ANION / : / Alginate production protein AlgE Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | |||||||||
Authors | Huang, C.-Y. / Boland, C. / Kaki, S.S. / Wang, M. / Olieric, V. / Caffrey, M. | |||||||||
Funding support | European Union, Ireland, 2items
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Citation | Journal: Crystals / Year: 2023 Title: Se-MAG Is a Convenient Additive for Experimental Phasing and Structure Determination of Membrane Proteins Crystallised by the Lipid Cubic Phase (In Meso) Method Authors: Boland, C. / Huang, C.Y. / Shanker Kaki, S. / Wang, M. / Olieric, V. / Caffrey, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q2o.cif.gz | 141.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q2o.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 8q2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q2o_validation.pdf.gz | 4 MB | Display | wwPDB validaton report |
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Full document | 8q2o_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 8q2o_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 8q2o_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/8q2o ftp://data.pdbj.org/pub/pdb/validation_reports/q2/8q2o | HTTPS FTP |
-Related structure data
Related structure data | 8q2pC C: citing same article (ref.) |
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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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53502.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: algE, alg76, PA3544 / Production host: Escherichia coli (E. coli) / References: UniProt: P18895 |
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-Non-polymers , 7 types, 341 molecules
#2: Chemical | ChemComp-FLC / | ||||||||||
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#3: Chemical | ChemComp-NA / #4: Chemical | #5: Chemical | ChemComp-IRY / [( Mass: 381.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C17H34O4Se / Feature type: SUBJECT OF INVESTIGATION #6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
-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: 2.25 Å3/Da / Density % sol: 45.24 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.6 Details: 41 %(v/v) PEG400, 100 mM LiSO4, and 0.1 M sodium citrate at pH 5.6 PH range: 5.6-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97794 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97794 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→44.63 Å / Num. obs: 102477 / % possible obs: 100 % / Redundancy: 45.88 % / Biso Wilson estimate: 21.87 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.21 / Net I/σ(I): 17.63 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 9.73 % / Mean I/σ(I) obs: 1.61 / Num. unique obs: 7616 / CC1/2: 0.66 / Rrim(I) all: 1.64 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→44.63 Å / SU ML: 0.2135 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.6501 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→44.63 Å
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Refine LS restraints |
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LS refinement shell |
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