+Open data
-Basic information
Entry | Database: PDB / ID: 6fqe | |||||||||
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Title | Phosphotriesterase PTE_A53_4 | |||||||||
Components | (Parathion hydrolase) x 2 | |||||||||
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: 1.75 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. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Phosphotriesterase PTE_A53_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 | 6fqe.cif.gz | 153 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fqe.ent.gz | 116.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fqe_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6fqe_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6fqe_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 6fqe_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/6fqe ftp://data.pdbj.org/pub/pdb/validation_reports/fq/6fqe | HTTPS FTP |
-Related structure data
Related structure data | 6fu6C 1hzyS 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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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 36756.648 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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#2: Protein | Mass: 36756.648 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 |
-Non-polymers , 5 types, 472 molecules
#3: Chemical | #4: Chemical | ChemComp-ZN / #5: Chemical | #6: Chemical | ChemComp-PEG / | #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: 2.13 Å3/Da / Density % sol: 42.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12% PEG 8000 0.05M Tris pH=7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5141 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5141 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30.143 Å / Num. obs: 58412 / % possible obs: 94.3 % / Redundancy: 7.6 % / Biso Wilson estimate: 15.38 Å2 / Rmerge(I) obs: 0.02559 / Net I/σ(I): 18.96 |
Reflection shell | Resolution: 1.75→1.813 Å / Redundancy: 7 % / Rmerge(I) obs: 0.1629 / Mean I/σ(I) obs: 4.57 / Num. unique obs: 5591 / % possible all: 90.59 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HZY Resolution: 1.75→30.143 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→30.143 Å
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Refine LS restraints |
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LS refinement shell |
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