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Yorodumi- PDB-7ec0: Crystal structure of juvenile hormone acid methyltransferase JHAM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ec0 | ||||||
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Title | Crystal structure of juvenile hormone acid methyltransferase JHAMT in complex with S-Adenosyl homocysteine and methyl farnesoate | ||||||
Components | Juvenile hormone acid methyltransferase | ||||||
Keywords | HORMONE / Juvenile hormone / Methyltransferase / Complex | ||||||
Function / homology | Methyl farnesoate / S-ADENOSYL-L-HOMOCYSTEINE Function and homology information | ||||||
Biological species | Bombyx mori (domestic silkworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.494 Å | ||||||
Authors | Guo, P.C. / Zhang, Y.S. / Zhang, L. / Xu, H.Y. / Xia, Q.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Structural basis for juvenile hormone biosynthesis by the juvenile hormone acid methyltransferase. Authors: Guo, P. / Zhang, Y. / Zhang, L. / Xu, H. / Zhang, H. / Wang, Z. / Jiang, Y. / Molloy, D. / Zhao, P. / Xia, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ec0.cif.gz | 567.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ec0.ent.gz | 479.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ec0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ec0_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 7ec0_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 7ec0_validation.xml.gz | 57.2 KB | Display | |
Data in CIF | 7ec0_validation.cif.gz | 74.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/7ec0 ftp://data.pdbj.org/pub/pdb/validation_reports/ec/7ec0 | HTTPS FTP |
-Related structure data
Related structure data | 7ebsC 7ebxSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 34054.812 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-SAH / #3: Chemical | ChemComp-J10 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | The sequence is corresponding to the entry of KWMTBOMO04857 in Silkbase, or the entry of ...The sequence is corresponding to the entry of KWMTBOMO04857 in Silkbase, or the entry of BMSK0004751.1 in the SilkDB 3.0. It is consist with the partial sequence of XP_037868953.1 (NCBI number, 16-282aa). The sequence contains tag residues MHHHHHHSSG | |
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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: 2.27 Å3/Da / Density % sol: 41.62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.15M DL-Malic acid pH 7.0, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→72.26 Å / Num. obs: 58792 / % possible obs: 99.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.062 / Χ2: 0.9 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.49→2.63 Å / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 8516 / Rrim(I) all: 0.792 / Χ2: 0.77 / % possible all: 99.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EBX Resolution: 2.494→72.26 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / ESU R: 0.934 / ESU R Free: 0.353 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.599 Å2
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Refinement step | Cycle: LAST / Resolution: 2.494→72.26 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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