+Open data
-Basic information
Entry | Database: PDB / ID: 4ttd | ||||||
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Title | Structure of a lysozyme antibody complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / affinity maturation | ||||||
Function / homology | Function and homology information Lactose synthesis / 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 ...Lactose synthesis / 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 | Homo sapiens (human) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å | ||||||
Authors | Wensley, B. | ||||||
Citation | Journal: To Be Published Title: Structure of a lysozyme antibody complex Authors: Wensley, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ttd.cif.gz | 217.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ttd.ent.gz | 179.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ttd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/4ttd ftp://data.pdbj.org/pub/pdb/validation_reports/tt/4ttd | 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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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Fragment: Residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme #2: Antibody | Mass: 23395.211 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #3: Antibody | Mass: 22854.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM PCTP pH 4.5, 25% w/v Peg3350, ethanol 5% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→44.41 Å / Num. obs: 57649 / % possible obs: 94.4 % / Redundancy: 1.64 % / Biso Wilson estimate: 55.73 Å2 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 1.64 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 1.5 / % possible all: 95 |
-Processing
Software | Name: BUSTER / Version: 2.11.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.15→41.22 Å / Cor.coef. Fo:Fc: 0.9256 / Cor.coef. Fo:Fc free: 0.9132 / SU R Cruickshank DPI: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.325 / SU Rfree Blow DPI: 0.229 / SU Rfree Cruickshank DPI: 0.236
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Displacement parameters | Biso mean: 53.41 Å2
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Refine analyze | Luzzati coordinate error obs: 0.437 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.15→41.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.21 Å / Total num. of bins used: 20
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