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Yorodumi- PDB-5k59: Crystal structure of LukGH from Staphylococcus aureus in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k59 | ||||||
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Title | Crystal structure of LukGH from Staphylococcus aureus in complex with a neutralising antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / toxin neutralizing monoclonal antibody / conformational epitope / X-ray crystal structure | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å | ||||||
Authors | Welin, M. / Logan, D.T. / Badarau, A. / Mirkina, I. / Zauner, G. / Dolezilkova, I. / Nagy, E. | ||||||
Citation | Journal: Mabs / Year: 2016 Title: Context matters: The importance of dimerization-induced conformation of the LukGH leukocidin of Staphylococcus aureus for the generation of neutralizing antibodies. Authors: Badarau, A. / Rouha, H. / Malafa, S. / Battles, M.B. / Walker, L. / Nielson, N. / Dolezilkova, I. / Teubenbacher, A. / Banerjee, S. / Maierhofer, B. / Weber, S. / Stulik, L. / Logan, D.T. / ...Authors: Badarau, A. / Rouha, H. / Malafa, S. / Battles, M.B. / Walker, L. / Nielson, N. / Dolezilkova, I. / Teubenbacher, A. / Banerjee, S. / Maierhofer, B. / Weber, S. / Stulik, L. / Logan, D.T. / Welin, M. / Mirkina, I. / Pleban, C. / Zauner, G. / Gross, K. / Jagerhofer, M. / Magyarics, Z. / Nagy, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k59.cif.gz | 790.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k59.ent.gz | 680 KB | Display | PDB format |
PDBx/mmJSON format | 5k59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/5k59 ftp://data.pdbj.org/pub/pdb/validation_reports/k5/5k59 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Uncharacterized leukocidin-like protein ... , 2 types, 4 molecules DCBA
#1: Protein | Mass: 37143.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria) Strain: USA300 / Gene: SAUSA300_1975 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FFA2, UniProt: Q2FWP0*PLUS #2: Protein | Mass: 35825.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria) Strain: USA300 / Gene: SAUSA300_1974 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FFA3 |
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-Antibody , 2 types, 4 molecules HELF
#3: Antibody | Mass: 24166.100 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO3E7 / Production host: Cricetulus griseus (Chinese hamster) #4: Antibody | Mass: 23338.846 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO3E7 / Production host: Cricetulus griseus (Chinese hamster) |
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-Non-polymers , 4 types, 7 molecules
#5: Chemical | ChemComp-CL / |
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#6: Chemical | ChemComp-PO4 / |
#7: Chemical | ChemComp-PG4 / |
#8: 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: 2.96 Å3/Da / Density % sol: 58.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.2 Details: Drop contained 200 nl Fab-LukGH at 1:1 ratio + 50 nl seed stock + 150 nl reservoir solution [0.3 M NaCl, 26% polyethylene glycol (PEG) 8000, 0.1 M phosphate citrate pH 4.2]. The seed ...Details: Drop contained 200 nl Fab-LukGH at 1:1 ratio + 50 nl seed stock + 150 nl reservoir solution [0.3 M NaCl, 26% polyethylene glycol (PEG) 8000, 0.1 M phosphate citrate pH 4.2]. The seed solution was obtained from 40 % PEG 300, 0.1 M phosphate-citrate pH 4.2, 0.3 M NaCl, 20 mM HEPES pH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2014 / Details: focusing mirrors |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→48.8 Å / Num. obs: 64655 / % possible obs: 99.3 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.84→2.91 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 1.4 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→48.54 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.35 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.8 Å2
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Refinement step | Cycle: 1 / Resolution: 2.84→48.54 Å
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Refine LS restraints |
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