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Yorodumi- PDB-3c7t: Crystal structure of the ecdysone phosphate phosphatase, EPPase, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c7t | ||||||
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Title | Crystal structure of the ecdysone phosphate phosphatase, EPPase, from Bombix mori in complex with tungstate | ||||||
Components | Ecdysteroid-phosphate phosphatase | ||||||
Keywords | HYDROLASE / phosphatase / ecdysone / 2H-phosphatase / PGM | ||||||
Function / homology | Function and homology information ecdysteroid-phosphate phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Bombyx mori (domestic silkworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å | ||||||
Authors | Chen, Y. / Carpino, N. / Nassar, N. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structural and functional characterization of the c-terminal domain of the ecdysteroid phosphate phosphatase from Bombyx mori reveals a new enzymatic activity. Authors: Chen, Y. / Jakoncic, J. / Wang, J. / Zheng, X. / Carpino, N. / Nassar, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c7t.cif.gz | 224.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c7t.ent.gz | 181.4 KB | Display | PDB format |
PDBx/mmJSON format | 3c7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c7t_validation.pdf.gz | 469.9 KB | Display | wwPDB validaton report |
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Full document | 3c7t_full_validation.pdf.gz | 482.2 KB | Display | |
Data in XML | 3c7t_validation.xml.gz | 44.2 KB | Display | |
Data in CIF | 3c7t_validation.cif.gz | 63.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/3c7t ftp://data.pdbj.org/pub/pdb/validation_reports/c7/3c7t | 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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3 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 29570.150 Da / Num. of mol.: 4 / Fragment: PGM homology domain (residues 69-331) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori (domestic silkworm) / Plasmid: pProEX-HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7YTB0 |
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-Non-polymers , 6 types, 635 molecules
#2: Chemical | ChemComp-WO4 / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-IOD / #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-MG / | #7: 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: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16% Peg8000, 0.2 M magnesium chloride, 0.1 M Tris-HCl, 5 mM sodium tungstate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 5, 2007 / Details: monochromator |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→32.2 Å / Num. all: 114147 / Num. obs: 114147 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.76→1.8 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 2.6 / Num. unique all: 7361 / Rsym value: 0.654 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.76→32.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.429 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.108 / 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: 24.714 Å2
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Refine analyze | Luzzati coordinate error free: 0.108 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→32.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.756→1.802 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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