+Open data
-Basic information
Entry | Database: PDB / ID: 5vph | |||||||||
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Title | CRYSTAL STRUCTURE OF DER P 1 COMPLEXED WITH FAB 4C1 | |||||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / DER P 1 / ALLERGEN-ANTIBODY COMPLEX / HYDROLASE-IMMUNE SYSTEM COMPLEX | |||||||||
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: 2.5 Å | |||||||||
Authors | Chruszcz, M. / Vailes, L.D. / Chapman, M.D. / Pomes, A. / Minor, W. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Molecular Determinants For Antibody Binding On Group 1 House Dust Mite Allergens. Authors: Chruszcz, M. / Pomes, A. / Glesner, J. / Vailes, L.D. / Osinski, T. / Porebski, P.J. / Majorek, K.A. / Heymann, P.W. / Platts-Mills, T.A. / Minor, W. / Chapman, M.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vph.cif.gz | 234.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vph.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 5vph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/5vph ftp://data.pdbj.org/pub/pdb/validation_reports/vp/5vph | HTTPS FTP |
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-Related structure data
Related structure data | 3rvtC 3rvuC 5vpgC 5vplC 3f5vS 3rvv 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25014.805 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 81-302 / Source method: isolated from a natural source Source: (natural) Dermatophagoides pteronyssinus (European house dust mite) References: UniProt: Q3HWZ5, UniProt: P08176*PLUS |
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-Antibody , 2 types, 2 molecules CD
#2: Antibody | Mass: 23937.645 Da / Num. of mol.: 1 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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#3: Antibody | Mass: 27677.270 Da / Num. of mol.: 1 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) |
-Non-polymers , 3 types, 202 molecules
#4: Chemical | ChemComp-CA / |
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#5: Chemical | ChemComp-EDO / |
#6: 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: 2.3 Å3/Da / Density % sol: 46.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 0.1M HEPES, 10% W/V PEG4000, 0.05M GLYGLYGLY, 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-BM / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 18, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 23380 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 55.5 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.596 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F5V, 3RVV Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 20.939 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.292 / 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: 55.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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