+Open data
-Basic information
Entry | Database: PDB / ID: 3dye | ||||||
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Title | Crystal structure of AED7-norepineprhine complex | ||||||
Components | D7 protein | ||||||
Keywords | odorant-binding protein / all-helical / secreted / Allergen | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aedes aegypti (yellow fever mosquito) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å | ||||||
Authors | Andersen, J.F. / Calvo, E. / Mans, B.J. / Ribeiro, J.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Multifunctionality and mechanism of ligand binding in a mosquito antiinflammatory protein Authors: Calvo, E. / Mans, B.J. / Ribeiro, J.M. / Andersen, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dye.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dye.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 3dye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/3dye ftp://data.pdbj.org/pub/pdb/validation_reports/dy/3dye | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35117.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Strain: Liverpool / Gene: D7 / Organ: kidney / Plasmid: VR2001 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P18153 | ||||||||
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#2: Chemical | ChemComp-BR / #3: Chemical | ChemComp-LNR / | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | THERE IS CHIRALITY ISSUE AT CAL CENTER OF LIGAND LNR | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16-20% PEG 6000, Tris HCl, 0.1 M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å |
Detector | Type: SBC CCD / Detector: CCD / Date: Mar 17, 2007 / Details: Si-111 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 31957 / Num. obs: 31957 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.068 / Χ2: 0.953 |
Reflection shell | Resolution: 1.75→1.82 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3098 / Χ2: 0.598 / % possible all: 97 |
-Processing
Software |
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Refinement | Resolution: 1.75→27.27 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.853 / SU B: 4.462 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.59 Å2 / Biso mean: 24.179 Å2 / Biso min: 4.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→27.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.799 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -5.7473 Å / Origin y: 4.1114 Å / Origin z: 12.7573 Å
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