+Open data
-Basic information
Entry | Database: PDB / ID: 3mq1 | ||||||
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Title | Crystal Structure of Dust Mite Allergen Der p 5 | ||||||
Components | Mite allergen Der p 5 | ||||||
Keywords | ALLERGEN / DUST MITE | ||||||
Function / homology | Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #970 / Mite allergen, group 5/21 / Mite allergen, group 5/21 superfamily / Mite allergen Blo t 5 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / PHOSPHATE ION / Mite allergen Der p 5 Function and homology information | ||||||
Biological species | Dermatophagoides pteronyssinus (European house dust mite) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Mueller, G.A. / Gosavi, R.A. / Krahn, J.M. / Edwards, L.L. / Cuneo, M.J. / Glesner, J. / Pomes, A. / Chapman, M.D. / London, R.E. / Pedersen, L.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Der p 5 crystal structure provides insight into the group 5 dust mite allergens. Authors: Mueller, G.A. / Gosavi, R.A. / Krahn, J.M. / Edwards, L.L. / Cuneo, M.J. / Glesner, J. / Pomes, A. / Chapman, M.D. / London, R.E. / Pedersen, L.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mq1.cif.gz | 265.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mq1.ent.gz | 219.5 KB | Display | PDB format |
PDBx/mmJSON format | 3mq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mq1_validation.pdf.gz | 520.4 KB | Display | wwPDB validaton report |
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Full document | 3mq1_full_validation.pdf.gz | 529.3 KB | Display | |
Data in XML | 3mq1_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 3mq1_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/3mq1 ftp://data.pdbj.org/pub/pdb/validation_reports/mq/3mq1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 12143.111 Da / Num. of mol.: 6 / Fragment: UNP residues 34-132 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite) Gene: DERP5 / Plasmid: PGEX4T3(tev) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P14004 #2: Chemical | ChemComp-MPD / ( #3: Chemical | ChemComp-MRD / ( #4: Chemical | ChemComp-PO4 / | #5: 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: 2.6 Å3/Da / Density % sol: 52.74 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 31.5% MPD, 90 mM Na/K phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: May 8, 2009 / Details: VariMax HF |
Radiation | Monochromator: VariMaxHF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 19292 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rsym value: 0.069 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1883 / Rsym value: 0.518 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Resolution: 2.8→33.598 Å / SU ML: 0.38 / σ(F): 0.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.539 Å2 / ksol: 0.287 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→33.598 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain F |