+Open data
-Basic information
Entry | Database: PDB / ID: 1jti | ||||||
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Title | Loop-inserted Structure of P1-P1' Cleaved Ovalbumin Mutant R339T | ||||||
Components | Ovalbumin | ||||||
Keywords | ALLERGEN / ovalbumin / loop insertion / non-inhibitory serpin | ||||||
Function / homology | Function and homology information intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / response to steroid hormone / embryo development ending in birth or egg hatching / response to corticosterone / monoatomic ion transport / phagocytic vesicle / early endosome lumen ...intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / response to steroid hormone / embryo development ending in birth or egg hatching / response to corticosterone / monoatomic ion transport / phagocytic vesicle / early endosome lumen / Neutrophil degranulation / response to progesterone / response to estrogen / protease binding / vesicle / intracellular membrane-bounded organelle / calcium ion binding / endoplasmic reticulum / extracellular space / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.3 Å | ||||||
Authors | Yamasaki, M. / Arii, Y. / Mikami, B. / Hirose, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Loop-inserted and thermostabilized structure of P1-P1' cleaved ovalbumin mutant R339T. Authors: Yamasaki, M. / Arii, Y. / Mikami, B. / Hirose, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jti.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jti.ent.gz | 126.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jti_validation.pdf.gz | 371.7 KB | Display | wwPDB validaton report |
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Full document | 1jti_full_validation.pdf.gz | 391.1 KB | Display | |
Data in XML | 1jti_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 1jti_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jti ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jti | 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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Unit cell |
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-Components
#1: Protein | Mass: 42765.848 Da / Num. of mol.: 2 / Mutation: R339T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: ovalbumin / Plasmid: PET-OVA(R339T) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01012 #2: 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: 2.46 Å3/Da / Density % sol: 49.99 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, Bis-Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 30 ℃ / pH: 6 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 15, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→15 Å / Num. all: 98045 / Num. obs: 36122 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.12 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.049 |
Reflection shell | Resolution: 2.24→2.384 Å / % possible all: 93.3 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 98045 / Rmerge(I) obs: 0.049 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 817933.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.2904 Å2 / ksol: 0.291263 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 10.3 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 41.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.295 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.261 |