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Yorodumi- PDB-3a1z: Crystal structure of juvenile hormone binding protein from silkworm -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a1z | ||||||
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Title | Crystal structure of juvenile hormone binding protein from silkworm | ||||||
Components | Hemolymph juvenile hormone binding protein | ||||||
Keywords | TRANSPORT PROTEIN / juvenile hormone | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bombyx mori (domestic silkworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å | ||||||
Authors | Suzuki, R. / Fujimoto, Z. / Shiotsuki, T. / Momma, M. / Tase, A. / Yamazaki, T. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Crystal structure of silkworm Bombyx mori JHBP in complex with 2-methyl-2,4-pentanediol: plasticity of JH-binding pocket and ligand-induced conformational change of the second cavity in JHBP Authors: Fujimoto, Z. / Suzuki, R. / Shiotsuki, T. / Tsuchiya, W. / Tase, A. / Momma, 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. #2: Journal: Insect Mol.Biol. / Year: 2001 Title: The juvenile hormone binding protein of silkworm haemolymph: gene and functional analysis Authors: Vermunt, A.M. / Kamimura, M. / Hirai, M. / Kiuchi, M. / Shiotsuki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a1z.cif.gz | 172.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a1z.ent.gz | 145.8 KB | Display | PDB format |
PDBx/mmJSON format | 3a1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a1z_validation.pdf.gz | 483.4 KB | Display | wwPDB validaton report |
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Full document | 3a1z_full_validation.pdf.gz | 539.6 KB | Display | |
Data in XML | 3a1z_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 3a1z_validation.cif.gz | 54.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/3a1z ftp://data.pdbj.org/pub/pdb/validation_reports/a1/3a1z | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 24781.092 Da / Num. of mol.: 4 / 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 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MPD / ( #4: Water | ChemComp-HOH / | Sequence details | THE NUMBER ZERO WAS SIMPLY SKIPPED IN RESIDUE NUMBERING TO CLARIFY THE EXPRESSION | |
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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: 3.06 Å3/Da / Density % sol: 59.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% MPD, 0.05M zinc acetate, 0.1M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 26, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. obs: 38636 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.59→2.69 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.1 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.59→49.49 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.897 / SU B: 10.286 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.479 / ESU R Free: 0.327 / 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 mean: 51.67 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.59→49.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.59→2.657 Å / Total num. of bins used: 20
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