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Yorodumi- PDB-6s3t: P46, an immunodominant surface protein from Mycoplasma hyopneumoniae -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s3t | ||||||||||||
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Title | P46, an immunodominant surface protein from Mycoplasma hyopneumoniae | ||||||||||||
Components |
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Keywords | PROTEIN BINDING / immunodominant surface protein Mycoplasma hyopneumoniae P46 Complex with monolonal antibody | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Mycoplasma hyopneumoniae J (bacteria) Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||||||||
Authors | Guasch, A. / Gonzalez-Gonzalez, L. / Fita, I. | ||||||||||||
Funding support | Spain, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Structure of P46, an immunodominant surface protein from Mycoplasma hyopneumoniae: interaction with a monoclonal antibody. Authors: Guasch, A. / Montane, J. / Moros, A. / Pinol, J. / Sitja, M. / Gonzalez-Gonzalez, L. / Fita, I. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6s3t.cif.gz | 769.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s3t.ent.gz | 504.4 KB | Display | PDB format |
PDBx/mmJSON format | 6s3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/6s3t ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s3t | HTTPS FTP |
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-Related structure data
Related structure data | 6rnnSC 6rqgSC 6ruxC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 42426.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma hyopneumoniae J (bacteria) / Gene: p46, MHJ_0511 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0C0J8 #2: Antibody | Mass: 26370.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #3: Antibody | Mass: 52172.977 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #4: Sugar | ChemComp-XYP / #5: Chemical | ChemComp-NA / Has ligand of interest | Y | |
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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: 3.53 Å3/Da / Density % sol: 65.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M MIB pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→29.3 Å / Num. obs: 83357 / % possible obs: 98.8 % / Redundancy: 1.9 % / CC1/2: 0.981 / Net I/σ(I): 5.51 |
Reflection shell | Resolution: 3.5→3.6 Å / Num. unique obs: 8278 / CC1/2: 0.292 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RQG, 6RNN Resolution: 3.5→29 Å / Cross valid method: FREE R-VALUE / σ(F): 2.4 / Phase error: 31.8932
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 103.39 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→29.3 Å
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