+Open data
-Basic information
Entry | Database: PDB / ID: 7pzo | ||||||
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Title | mite allergen Der p 3 from Dermatophagoides pteronyssinus | ||||||
Components | mite allergen Der p 3 | ||||||
Keywords | ALLERGEN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Dermatophagoides pteronyssinus (European house dust mite) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Timofeev, V.I. / Shevtsov, M.B. / Abramchik, Y.A. / Mikheeva, O.O. / Kostromina, M.A. / Lykoshin, D.D. / Zayats, E.A. / Zavriev, S.K. / Esipov, R.S. / Kuranova, I.P. | ||||||
Funding support | 1items
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Citation | Journal: J.Biomol.Struct.Dyn. / Year: 2018 Title: Structural plasticity and thermal stability of the histone-like protein from Spiroplasma melliferum are due to phenylalanine insertions into the conservative scaffold. Authors: Timofeev, V.I. / Altukhov, D.A. / Talyzina, A.A. / Agapova, Y.K. / Vlaskina, A.V. / Korzhenevskiy, D.A. / Kleymenov, S.Y. / Bocharov, E.V. / Rakitina, T.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pzo.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pzo.ent.gz | 75.8 KB | Display | PDB format |
PDBx/mmJSON format | 7pzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pzo_validation.pdf.gz | 448.3 KB | Display | wwPDB validaton report |
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Full document | 7pzo_full_validation.pdf.gz | 455.5 KB | Display | |
Data in XML | 7pzo_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 7pzo_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/7pzo ftp://data.pdbj.org/pub/pdb/validation_reports/pz/7pzo | HTTPS FTP |
-Related structure data
Related structure data | 5oguC 3p95S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24773.096 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite) Gene: LOC113796035 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6P6YAT6 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.14 Å3/Da / Density % sol: 42.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96772 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96772 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 20151 / % possible obs: 96.3 % / Redundancy: 1.95 % / CC1/2: 0.973 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.205 / Net I/σ(I): 6.63 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 1.99 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.65 / Num. unique obs: 1466 / CC1/2: 0.751 / Rrim(I) all: 0.728 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P95 Resolution: 2.25→28.58 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.881 / SU B: 8.669 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.402 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.27 Å2 / Biso mean: 28.374 Å2 / Biso min: 8.42 Å2
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Refinement step | Cycle: final / Resolution: 2.25→28.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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