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Yorodumi- PDB-5vcn: THE CRYSTAL STRUCTURE OF DER P 1 ALLERGEN COMPLEXED WITH FAB FRAG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vcn | |||||||||
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Title | THE CRYSTAL STRUCTURE OF DER P 1 ALLERGEN COMPLEXED WITH FAB FRAGMENT OF MAB 5H8 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / ALLERGEN / ANTIBODY | |||||||||
Function / homology | Function and homology information peptidase 1 (mite) / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Dermatophagoides pteronyssinus (European house dust mite) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Osinski, T. / Majorek, K.A. / Pomes, A. / Offermann, L.R. / Osinski, S. / Glesner, J. / Vailes, L.D. / Chapman, M.D. / Minor, W. / Chruszcz, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Immunol. / Year: 2015 Title: Structural Analysis of Der p 1-Antibody Complexes and Comparison with Complexes of Proteins or Peptides with Monoclonal Antibodies. Authors: Osinski, T. / Pomes, A. / Majorek, K.A. / Glesner, J. / Offermann, L.R. / Vailes, L.D. / Chapman, M.D. / Minor, W. / Chruszcz, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vcn.cif.gz | 495.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vcn.ent.gz | 405.8 KB | Display | PDB format |
PDBx/mmJSON format | 5vcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vcn_validation.pdf.gz | 504.1 KB | Display | wwPDB validaton report |
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Full document | 5vcn_full_validation.pdf.gz | 526.5 KB | Display | |
Data in XML | 5vcn_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 5vcn_validation.cif.gz | 64.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/5vcn ftp://data.pdbj.org/pub/pdb/validation_reports/vc/5vcn | HTTPS FTP |
-Related structure data
Related structure data | 4pozC 5vcoC 3f5vS 3rvtS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
-Antibody , 2 types, 4 molecules CEDF
#2: Antibody | Mass: 23232.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: MUS MUSCULUS (house mouse) #3: Antibody | Mass: 28000.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HYBRIDOMA / Production host: MUS MUSCULUS (house mouse) |
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-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 25014.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Dermatophagoides pteronyssinus (European house dust mite) References: UniProt: Q3HWZ5, UniProt: P08176*PLUS #7: Sugar | |
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-Non-polymers , 4 types, 80 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #8: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 46.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 MM MES, 10% W/V PEG 6000, 5% MPD, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 28001 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Net I/σ(I): 10 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.653 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F5V, 3RVT Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.857 / SU B: 50.017 / SU ML: 0.432 / Cross valid method: THROUGHOUT / ESU R Free: 0.492 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.05 Å2
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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