+Open data
-Basic information
Entry | Database: PDB / ID: 6zc1 | ||||||
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Title | Crystal structure of RahU protein from Pseudomonas aeruginosa | ||||||
Components | RahU protein | ||||||
Keywords | TOXIN / Aegerolysin / Pseudomonas aeruginosa / RahU protein / protein-membrane interaction | ||||||
Function / homology | Hemolysin, aegerolysin type / Aegerolysin / hemolysis by symbiont of host erythrocytes / glycolipid binding / Aegerolysin Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.27 Å | ||||||
Authors | Podobnik, M. / Anderluh, G. / Lenarcic, T. | ||||||
Funding support | Slovenia, 1items
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Citation | Journal: Sci Rep / Year: 2021 Title: Crystal structure of RahU, an aegerolysin protein from the human pathogen Pseudomonas aeruginosa, and its interaction with membrane ceramide phosphorylethanolamine. Authors: Kocar, E. / Lenarcic, T. / Hodnik, V. / Panevska, A. / Huang, Y. / Bajc, G. / Kostanjsek, R. / Naren, A.P. / Macek, P. / Anderluh, G. / Sepcic, K. / Podobnik, M. / Butala, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zc1.cif.gz | 75.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zc1.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zc1_validation.pdf.gz | 402.2 KB | Display | wwPDB validaton report |
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Full document | 6zc1_full_validation.pdf.gz | 402.4 KB | Display | |
Data in XML | 6zc1_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 6zc1_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/6zc1 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/6zc1 | HTTPS FTP |
-Related structure data
Related structure data | 6zc2C 4oebS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15255.614 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0122 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I710 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: di-Sodium tartrate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 16, 2015 Details: a vertical collimating mirror, a double-crystal Si(111) monochromator, a bendable focussing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.27→30.87 Å / Num. obs: 39465 / % possible obs: 93.6 % / Redundancy: 6.479 % / Biso Wilson estimate: 12.18 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.104 / Χ2: 0.973 / Net I/σ(I): 11.8 / Num. measured all: 255698 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OEB Resolution: 1.27→30.87 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.07 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.38 Å2 / Biso mean: 16.9725 Å2 / Biso min: 7.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.27→30.87 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 25.1309 Å / Origin y: 36.6105 Å / Origin z: 25.77 Å
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Refinement TLS group |
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