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Yorodumi- PDB-7acg: In meso structure of the alginate exporter, AlgE, from Pseudomona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7acg | ||||||
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Title | In meso structure of the alginate exporter, AlgE, from Pseudomonas aeruginosa in 9.8 monoacylglycerol | ||||||
Components | Alginate biosynthesis protein AlgE | ||||||
Keywords | MEMBRANE PROTEIN / Transporter / Barrel | ||||||
Function / homology | Alginate export domain / Alginate export / alginic acid biosynthetic process / cell outer membrane / CITRIC ACID / Chem-LH9 / Alginate biosynthesis protein AlgE / Alginate production protein AlgE Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Smithers, L. / van Dalsen, L. / Boland, C. / Caffrey, M. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: Cryst.Growth Des. / Year: 2020 Title: 9.8 MAG. A new host lipid for in meso (lipid cubic phase) crystallization of integral membrane proteins Authors: van Dalsen, L. / Smithers, L. / Boland, C. / Weichert, D. / Caffrey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7acg.cif.gz | 244.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7acg.ent.gz | 162.9 KB | Display | PDB format |
PDBx/mmJSON format | 7acg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7acg_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7acg_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7acg_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 7acg_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/7acg ftp://data.pdbj.org/pub/pdb/validation_reports/ac/7acg | HTTPS FTP |
-Related structure data
Related structure data | 7aciC 4afkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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 (bacteria) Gene: algE, CGU42_05540, EQH76_07525, F3H14_18260, FC629_07390, GNQ48_06715, IPC1323_01805, IPC1509_00845, IPC669_06720, NCTC12934_05462, NCTC13437_03064, PaeAG1_01671, PAMH19_1548, RW109_RW109_02276 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A080VSR9, UniProt: P18895*PLUS |
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-Non-polymers , 8 types, 131 molecules
#2: Chemical | ChemComp-LH9 / [( #3: Chemical | ChemComp-1PE / | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-C8E / ( | #6: Chemical | ChemComp-CIT / | #7: Chemical | ChemComp-PG0 / | #8: Chemical | #9: 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: 2.21 Å3/Da / Density % sol: 44.26 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: PEG400, lithium sulphate, ammonium sulphate, sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→44.37 Å / Num. obs: 39482 / % possible obs: 99.08 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.24 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.35 |
Reflection shell | Resolution: 1.85→1.916 Å / Mean I/σ(I) obs: 1.36 / Num. unique obs: 3904 / CC1/2: 0.61 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AFK Resolution: 1.85→44.37 Å / SU ML: 0.2292 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4007 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: 37.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→44.37 Å
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Refine LS restraints |
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LS refinement shell |
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