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- PDB-7v25: Crystal Structure of phthalate dioxygenase in complex with phthalate -
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Open data
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Basic information
Entry | Database: PDB / ID: 7v25 | ||||||
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Title | Crystal Structure of phthalate dioxygenase in complex with phthalate | ||||||
![]() | Rieske (2Fe-2S) domain protein | ||||||
![]() | OXIDOREDUCTASE / dioxygenase / bacterial protein / metalloprotein / Rieske domain | ||||||
Function / homology | ![]() 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mahto, J.K. / Kumar, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular insights into substrate recognition and catalysis by phthalate dioxygenase from Comamonas testosteroni. Authors: Mahto, J.K. / Neetu, N. / Waghmode, B. / Kuatsjah, E. / Sharma, M. / Sircar, D. / Sharma, A.K. / Tomar, S. / Eltis, L.D. / Kumar, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 509.9 KB | Display | ![]() |
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PDB format | ![]() | 417.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7fhrSC ![]() 7fjlC ![]() 7v28C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 49168.383 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 14576 / KF-1 / Gene: CtesDRAFT_PD2022 / Production host: ![]() ![]() #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-FES / #4: Chemical | ChemComp-PHT / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG4000, calcium chloride, magnesium chloride, sodium potassium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2020 |
Radiation | Monochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→159.88 Å / Num. obs: 88962 / % possible obs: 98.1 % / Redundancy: 1.9 % / CC1/2: 0.995 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.74→2.79 Å / Num. unique obs: 4664 / CC1/2: 0.805 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7FHR Resolution: 2.74→159.88 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.825 / SU B: 15.653 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.548 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 224.68 Å2 / Biso mean: 50.688 Å2 / Biso min: 12.35 Å2
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Refinement step | Cycle: final / Resolution: 2.74→159.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.74→2.809 Å / Rfactor Rfree error: 0
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