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Yorodumi- PDB-6p4a: HyHEL10 Fab complexed with hen egg lysozyme carrying two mutation... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p4a | ||||||
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Title | HyHEL10 Fab complexed with hen egg lysozyme carrying two mutations (HEL2x-rigid): R21Q and R73E | ||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / HyHEL10 / HEL2x-rigid / antibody-antigen / HyHEL10-HEL2x / HYDROLASE-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Langley, D.B. / Christ, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Conformational diversity facilitates antibody mutation trajectories and discrimination between foreign and self-antigens. Authors: Burnett, D.L. / Schofield, P. / Langley, D.B. / Jackson, J. / Bourne, K. / Wilson, E. / Porebski, B.T. / Buckle, A.M. / Brink, R. / Goodnow, C.C. / Christ, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p4a.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p4a.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 6p4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/6p4a ftp://data.pdbj.org/pub/pdb/validation_reports/p4/6p4a | HTTPS FTP |
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-Related structure data
Related structure data | 6p4bC 6p4cC 6p4dC 3d9aS 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: Antibody | Mass: 23552.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: LC / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: A0A0E4B213 |
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#2: Antibody | Mass: 24327.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) |
#3: Protein | Mass: 14274.016 Da / Num. of mol.: 1 / Mutation: R21Q, R73E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P00698, lysozyme |
#4: 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: 2.1 Å3/Da / Density % sol: 41.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Bis-Tris propane, pH 7.0, 22% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→48.5 Å / Num. obs: 26223 / % possible obs: 99.4 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Rrim(I) all: 0.102 / Net I/σ(I): 11.9 / Num. measured all: 178665 / Scaling rejects: 17 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3D9A Resolution: 2.2→48.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.174 / SU ML: 0.161 / SU R Cruickshank DPI: 0.0795 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.057 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 101.8 Å2 / Biso mean: 37.684 Å2 / Biso min: 20.11 Å2
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Refinement step | Cycle: final / Resolution: 2.2→48.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.201→2.258 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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