+Open data
-Basic information
Entry | Database: PDB / ID: 6pzl | |||||||||
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Title | P. mirabilis hemolysin A mutant - Q125A | |||||||||
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: 1.17 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 the HpmA265 Q125A variant Authors: Weaver, T.M. / Novak, W.R.P. / Grilley, D.P. / Wimmer, M.R. / Woods, C.N. / Bhattacharyya, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pzl.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pzl.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 6pzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/6pzl ftp://data.pdbj.org/pub/pdb/validation_reports/pz/6pzl | HTTPS FTP |
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-Related structure data
Related structure data | 6q0pC 4w8qS 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
#1: Protein | Mass: 25422.072 Da / Num. of mol.: 1 / Mutation: Q125A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: hpmA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16466 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.96 % |
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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: 19-BM / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→32.7 Å / Num. obs: 71123 / % possible obs: 87.2 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.012 / Net I/σ(I): 44.2 |
Reflection shell | Resolution: 1.17→1.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2859 / Rpim(I) all: 0.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4W8Q Resolution: 1.17→32.677 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.31 / 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: 51.12 Å2 / Biso mean: 16.588 Å2 / Biso min: 5.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.17→32.677 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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