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Yorodumi- PDB-6p4b: HyHEL10 fab variant HyHEL10-4x (heavy chain mutations L4F, Y33H, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p4b | ||||||
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Title | HyHEL10 fab variant HyHEL10-4x (heavy chain mutations L4F, Y33H, S56N, and Y58F) bound to hen egg lysozyme variant HEL2x-flex (mutations R21Q, R73E, C76S, and C94S) | ||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / HEL2x-flex / HyHEL10-4x / Fab / antigen-antibody / 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: 1.9 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 | 6p4b.cif.gz | 230.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p4b.ent.gz | 181.2 KB | Display | PDB format |
PDBx/mmJSON format | 6p4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/6p4b ftp://data.pdbj.org/pub/pdb/validation_reports/p4/6p4b | HTTPS FTP |
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-Related structure data
Related structure data | 6p4aC 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23552.857 Da / Num. of mol.: 2 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 #2: Antibody | Mass: 24347.918 Da / Num. of mol.: 2 / Mutation: L4F, Y33H, S56N, Y58F 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: 14241.885 Da / Num. of mol.: 2 / Mutation: R21Q, R73E, C76S, C94S 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: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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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: 2.38 Å3/Da / Density % sol: 48.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM citrate, pH 4.2, 1 M lithium chloride, 11% w/v 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: Mar 16, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.81→37.25 Å / Num. obs: 107151 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 11 / Num. measured all: 710161 / Scaling rejects: 47 | ||||||||||||||||||||||||||||||
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: 1.9→34.91 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.079 / SU ML: 0.118 / SU R Cruickshank DPI: 0.1599 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.149 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: 100.36 Å2 / Biso mean: 30.704 Å2 / Biso min: 13.22 Å2
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Refinement step | Cycle: final / Resolution: 1.9→34.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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