+Open data
-Basic information
Entry | Database: PDB / ID: 5iyu | ||||||
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Title | AlgE_CIM | ||||||
Components | Alginate production protein AlgE | ||||||
Keywords | MEMBRANE PROTEIN / alginate transporter | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Ma, P. / Weichert, D. | ||||||
Citation | Journal: Nat Protoc / Year: 2017 Title: The cubicon method for concentrating membrane proteins in the cubic mesophase. Authors: Ma, P. / Weichert, D. / Aleksandrov, L.A. / Jensen, T.J. / Riordan, J.R. / Liu, X. / Kobilka, B.K. / Caffrey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iyu.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iyu.ent.gz | 77.5 KB | Display | PDB format |
PDBx/mmJSON format | 5iyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iyu_validation.pdf.gz | 981 KB | Display | wwPDB validaton report |
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Full document | 5iyu_full_validation.pdf.gz | 991.8 KB | Display | |
Data in XML | 5iyu_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 5iyu_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/5iyu ftp://data.pdbj.org/pub/pdb/validation_reports/iy/5iyu | HTTPS FTP |
-Related structure data
Related structure data | 5d6iC 5d6kC 5d6lC 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: 54481.355 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 , 5 types, 44 molecules
#2: Chemical | #3: Chemical | ChemComp-OLC / ( | #4: Chemical | #5: Chemical | ChemComp-NA / | #6: 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: 2.14 Å3/Da / Density % sol: 42.65 % |
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Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase Details: 38 %(v/v) PEG 400, 0.1 M NaCitrate pH 5.6 and 0.1 M bis-tris pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9993 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9993 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→44.32 Å / Num. obs: 12694 / % possible obs: 99.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.7 |
Reflection shell | Rmerge(I) obs: 0.598 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AFK Resolution: 2.7→44.32 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→44.32 Å
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Refine LS restraints |
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LS refinement shell |
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