+Open data
-Basic information
Entry | Database: PDB / ID: 6g3m | ||||||
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Title | Phosphotriesterase PTE_C23M_4 | ||||||
Components | Parathion hydrolase | ||||||
Keywords | HYDROLASE / Metalloenzyme / TIM barrel | ||||||
Function / homology | Function and homology information aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Brevundimonas diminuta (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.665 Å | ||||||
Authors | Dym, O. / Aggarwal, N. / Albeck, S. / Unger, T. / Hamer Rogotner, S. / Silman, I. / Leader, H. / Ashani, Y. / Goldsmith, M. / Greisen, P. ...Dym, O. / Aggarwal, N. / Albeck, S. / Unger, T. / Hamer Rogotner, S. / Silman, I. / Leader, H. / Ashani, Y. / Goldsmith, M. / Greisen, P. / Tawfik, D. / Sussman, L.J. | ||||||
Citation | Journal: To Be Published Title: Phosphotriesterase PTE_C23M_4 Authors: Dym, O. / Aggarwal, N. / Albeck, S. / Unger, T. / Hamer Rogotner, S. / Silman, I. / Leader, H. / Ashani, Y. / Goldsmith, M. / Greisen, P. / Tawfik, D. / Sussman, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g3m.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g3m.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 6g3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/6g3m ftp://data.pdbj.org/pub/pdb/validation_reports/g3/6g3m | HTTPS FTP |
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-Related structure data
Related structure data | 1hyzS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35834.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Gene: opd / Production host: Escherichia coli (E. coli) / References: UniProt: P0A434, aryldialkylphosphatase |
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-Non-polymers , 8 types, 324 molecules
#2: Chemical | ChemComp-FMT / | ||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-VX / | #5: Chemical | ChemComp-E8N / | #6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris pH=8 1M (NH4)2SO4 12% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.541 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.665→22.96 Å / Num. obs: 54190 / % possible obs: 98.44 % / Observed criterion σ(F): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 18.76 Å2 / Rmerge(I) obs: 0.02787 / Net I/σ(I): 11.93 |
Reflection shell | Resolution: 1.665→1.724 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.2089 / Mean I/σ(I) obs: 2.95 / Num. unique obs: 5181 / % possible all: 96.59 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HYZ Resolution: 1.665→22.96 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.388 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.072 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.205 Å2
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Refinement step | Cycle: 1 / Resolution: 1.665→22.96 Å
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Refine LS restraints |
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