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Yorodumi- PDB-1ri8: Crystal Structure of the Camelid Single Domain Antibody 1D2L19 in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ri8 | ||||||
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Title | Crystal Structure of the Camelid Single Domain Antibody 1D2L19 in complex with Hen Egg White Lysozyme | ||||||
Components |
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Keywords | IMMUNE SYSTEM/HYDROLASE / beta sandwich / immunoglobulin fold / VHH-lysozyme complex / alpha-beta orthogonal bundle / IMMUNE SYSTEM-HYDROLASE 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 | Camelus dromedarius (Arabian camel) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | De Genst, E. / Silence, K. / Ghahroudi, M.A. / Decanniere, K. / Loris, R. / Kinne, J. / Wyns, L. / Muyldermans, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Strong in vivo maturation compensates for structurally restricted H3 loops in antibody repertoires. Authors: De Genst, E. / Silence, K. / Ghahroudi, M.A. / Decanniere, K. / Loris, R. / Kinne, J. / Wyns, L. / Muyldermans, S. | ||||||
History |
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Remark 999 | SEQUENCE The sequence of camelid heavy chain antibody (chain A) is not available in any reference ...SEQUENCE The sequence of camelid heavy chain antibody (chain A) is not available in any reference sequence database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ri8.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ri8.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ri8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/1ri8 ftp://data.pdbj.org/pub/pdb/validation_reports/ri/1ri8 | HTTPS FTP |
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-Related 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: 14717.281 Da / Num. of mol.: 1 / Fragment: VHH domain, VARIABLE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Tissue: Blood Lymphocytes / Plasmid: pHEN / Production host: Escherichia coli (E. coli) / Strain (production host): WK6Su |
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#2: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: Egg White / References: UniProt: P00698, lysozyme |
#3: Chemical | ChemComp-GOL / |
#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: 2.47 Å3/Da / Density % sol: 50.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, lithium sulphate, Tris-HCl, glycerol, sodium chloride, potassium phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2002 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. all: 25306 / Num. obs: 24895 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.7 / Num. unique all: 2178 / Rsym value: 0.25 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→29.17 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1680835.14 / Data cutoff high rms absF: 1680835.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.6513 Å2 / ksol: 0.40439 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→29.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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