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Yorodumi- PDB-4pgj: Human heavy-chain domain antibody in complex with hen egg-white l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pgj | ||||||
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Title | Human heavy-chain domain antibody in complex with hen egg-white lysozyme | ||||||
Components |
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Keywords | IMMUNE SYSTEM/HYDROLASE / antibody human dAb cleft binder dAb-HEL complex / IMMUNE SYSTEM-HYDROLASE complex | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Christ, D. / Langley, D.B. / Rouet, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Fully Human VH Single Domains That Rival the Stability and Cleft Recognition of Camelid Antibodies. Authors: Rouet, R. / Dudgeon, K. / Christie, M. / Langley, D. / Christ, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pgj.cif.gz | 180.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pgj.ent.gz | 144.1 KB | Display | PDB format |
PDBx/mmJSON format | 4pgj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/4pgj ftp://data.pdbj.org/pub/pdb/validation_reports/pg/4pgj | HTTPS FTP |
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-Related 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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Details | Authors report assembly confirmed by gel filtration and MALLS |
-Components
#1: Antibody | Mass: 13173.522 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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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: 2.61 Å3/Da / Density % sol: 52.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: Protein at 4.4 mg/mL in 50 mM Tris (pH 7.5) amd 150 mM NaCl. Well solution contained 28% (w/v) PEG1500, 100 mM Na-citrate (pH 5.4). 400 nL of well solution and protein solution were combined. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→49.08 Å / Num. obs: 16831 / % possible obs: 99.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 9 |
-Processing
Software | Name: REFMAC / Version: 5.6.0111 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.6→49.08 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.879 / SU B: 24.287 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.699 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.675 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→49.08 Å
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