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Yorodumi- PDB-3aot: Crystal structure of juvenile hormone binding protein from silkwo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aot | ||||||
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Title | Crystal structure of juvenile hormone binding protein from silkworm in its apo form | ||||||
Components | Hemolymph juvenile hormone binding protein | ||||||
Keywords | Hormone binding protein / Beta-barrel / juvenile hormone / Hemolymph | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bombyx mori (domestic silkworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Fujimoto, Z. / Suzuki, R. / Shiotsuki, T. / Momma, M. / Yamazaki, T. | ||||||
Citation | Journal: Sci Rep / Year: 2011 Title: Structural mechanism of JH delivery in hemolymph by JHBP of silkworm, Bombyx mori. Authors: Suzuki, R. / Fujimoto, Z. / Shiotsuki, T. / Tsuchiya, W. / Momma, M. / Tase, A. / Miyazawa, M. / Yamazaki, T. #1: Journal: Biomol.Nmr Assign. / Year: 2009 Title: NMR assignments of juvenile hormone binding protein in complex with JH III Authors: Suzuki, R. / Tase, A. / Fujimoto, Z. / Shiotsuki, T. / Yamazaki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aot.cif.gz | 56.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aot.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 3aot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aot_validation.pdf.gz | 458.2 KB | Display | wwPDB validaton report |
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Full document | 3aot_full_validation.pdf.gz | 463.1 KB | Display | |
Data in XML | 3aot_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 3aot_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/3aot ftp://data.pdbj.org/pub/pdb/validation_reports/ao/3aot | HTTPS FTP |
-Related structure data
Related structure data | 2rqfC 3aosSC 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
#1: Protein | Mass: 24781.092 Da / Num. of mol.: 1 / Fragment: UNP residues 19-243 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: hJHBP / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9U556 | ||||||||
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#2: Chemical | ChemComp-PG4 / #3: Chemical | ChemComp-PGE / | #4: Chemical | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 50% PEG 200, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 19, 2010 |
Radiation | Monochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 17925 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 20.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 57.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 11.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AOS Resolution: 2.2→37.86 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.509 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.181 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.982 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1233 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→37.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.197→2.254 Å / Total num. of bins used: 20
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