+Open data
-Basic information
Entry | Database: PDB / ID: 6pyk | |||||||||
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Title | P. mirabilis hemolysin A mutant - F80L | |||||||||
Components | Hemolysin | |||||||||
Keywords | TOXIN / hemolysin / two-partner secretion / beta-helix / protein secretion | |||||||||
Function / homology | Function and homology information catalytic activity / cell outer membrane / toxin activity / killing of cells of another organism Similarity search - Function | |||||||||
Biological species | Proteus mirabilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | |||||||||
Authors | Weaver, T.M. / Novak, W.R.P. / Bhattacharyya, B. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Structure of truncated hemolysin A variant F80L Authors: Weaver, T.M. / Novak, W.R.P. / Bhattacharyya, B. / Woods, C.N. / Grilley, D.P. / Wimmer, M.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pyk.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pyk.ent.gz | 83.7 KB | Display | PDB format |
PDBx/mmJSON format | 6pyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/6pyk ftp://data.pdbj.org/pub/pdb/validation_reports/py/6pyk | HTTPS FTP |
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-Related structure data
Related structure data | 3fy3S S: Starting model for refinement |
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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
#1: Protein | Mass: 25445.107 Da / Num. of mol.: 1 / Mutation: F80L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: hpmA / Plasmid: pET24a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16466 |
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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: 2.02 Å3/Da / Density % sol: 39.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 20, 2015 / Details: Beryllium Lenses |
Radiation | Monochromator: Double crystal cry-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→34.011 Å / Num. obs: 44578 / % possible obs: 99.3 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.034 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.35→1.39 Å / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4273 / Rpim(I) all: 0.331 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FY3 Resolution: 1.35→34.011 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 161.78 Å2 / Biso mean: 21.3845 Å2 / Biso min: 8.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→34.011 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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