+Open data
-Basic information
Entry | Database: PDB / ID: 2j88 | ||||||
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Title | Hyaluronidase in complex with a monoclonal IgG Fab fragment | ||||||
Components |
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Keywords | HYDROLASE / GLYCOPROTEIN / GLYCOSIDASE FAMILY 56 / ZYMOGEN / ALLERGEN / 7- STRANDED (BETA/ALPHA) TIM BARREL / GLYCOSIDASE / IMMUNOGLOBULIN DOMAIN | ||||||
Function / homology | Function and homology information hyaluronoglucosaminidase / hyalurononglucosaminidase activity / defense response / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | APIS MELLIFERA (honey bee) MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Padavattan, S. / Schirmer, T. / Markovic-Housley, Z. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Identification of a B-Cell Epitope of Hyaluronidase, a Major Bee Venom Allergen, from its Crystal Structure in Complex with a Specific Fab. Authors: Padavattan, S. / Schirmer, T. / Schmidt, M. / Akdis, C. / Valenta, R. / Mittermann, I. / Soldatova, L. / Slater, J. / Mueller, U. / Markovic-Housley, Z. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j88.cif.gz | 141.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j88.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 2j88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/2j88 ftp://data.pdbj.org/pub/pdb/validation_reports/j8/2j88 | 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: Protein | Mass: 40901.332 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-382 Source method: isolated from a genetically manipulated source Source: (gene. exp.) APIS MELLIFERA (honey bee) / Production host: TRICHOPLUSIA NI (cabbage looper) / Variant (production host): HIGH FIVE / References: UniProt: Q08169, hyaluronoglucosaminidase |
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#2: Antibody | Mass: 20506.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: HYBRIDOMA |
#3: Antibody | Mass: 23592.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: HYBRIDOMA |
#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: 3.9 Å3/Da / Density % sol: 69 % |
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Crystal grow | pH: 9.5 / Details: 10% PEG 8000, 0.2M NACL, 0.1M CHES PH9.5, pH 9.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 24, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→63.63 Å / Num. obs: 32047 / % possible obs: 85.4 % / Observed criterion σ(I): 0 / Redundancy: 3.17 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.98 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.19 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.15 / % possible all: 81.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: PDB ENTRIES 1FCQ, 1A7Q, 15C8 Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.885 / SU B: 16.798 / SU ML: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.416 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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