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- PDB-4u3x: Structure of a human VH antibody domain binding to the cleft of h... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4u3x | ||||||
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Title | Structure of a human VH antibody domain binding to the cleft of hen egg lysozyme | ||||||
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![]() | IMMUNE SYSTEM / Human VH domain antibody / Phage display / Antibody-antigen complex structure / HYDROLASE-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rouet, R. / Langley, D.B. / Christ, D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.2 KB | Display | ![]() |
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PDB format | ![]() | 152.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4pgjC ![]() 1lyzS ![]() 1ohqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 13173.522 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 300 mM sodium citrate, 16% PEG 3350 / PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→97.14 Å / Num. obs: 24456 / % possible obs: 98.6 % / Redundancy: 1.5 % / Net I/σ(I): 2.4 |
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Processing
Software | Name: REFMAC / Version: 5.8.0071 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Starting model: 1LYZ, 1OHQ Resolution: 2.26→97.14 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.892 / SU B: 15.494 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 14.923 Å2
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Refinement step | Cycle: 1 / Resolution: 2.26→97.14 Å
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Refine LS restraints |
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