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Yorodumi- PDB-5vco: THE CRYSTAL STRUCTURE OF DER P 1 ALLERGEN COMPLEXED WITH FAB FRAG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vco | |||||||||
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Title | THE CRYSTAL STRUCTURE OF DER P 1 ALLERGEN COMPLEXED WITH FAB FRAGMENT OF MAB 10B9 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / ALLERGEN / ANTIBODY | |||||||||
Function / homology | Function and homology information peptidase 1 (mite) / cysteine-type peptidase activity / proteolysis / extracellular region / 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: 2.74 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 | 5vco.cif.gz | 485.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vco.ent.gz | 398.4 KB | Display | PDB format |
PDBx/mmJSON format | 5vco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/5vco ftp://data.pdbj.org/pub/pdb/validation_reports/vc/5vco | HTTPS FTP |
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-Related structure data
Related structure data | 4pozC 5vcnC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
-Antibody , 2 types, 4 molecules ACBD
#1: Antibody | Mass: 23280.555 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) #2: Antibody | Mass: 24135.102 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 EF
#3: 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 #4: Sugar | |
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-Non-polymers , 2 types, 24 molecules
#5: Chemical | #6: 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: 2.39 Å3/Da / Density % sol: 48.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100 MM NA ACETATE, 8% W/V PEG 4000, 15% MPD, PH 4.5 PH range: 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.51201 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2011 / Details: BERYLLIUM LENSES |
Radiation | Monochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.51201 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→50 Å / Num. obs: 36141 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 55.2 Å2 / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.74→2.79 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.684 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F5V, 3RVT Resolution: 2.74→47.26 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.89 / SU B: 33.171 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.393 / 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: 46.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.74→47.26 Å
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Refine LS restraints |
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