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Yorodumi- PDB-7vju: Crystal Structure of terephthalate dioxygenase from Comamonas tes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vju | ||||||
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Title | Crystal Structure of terephthalate dioxygenase from Comamonas testosteroni KF1 | ||||||
Components |
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Keywords | OXIDOREDUCTASE / dioxygenase / bacterial protein / metalloprotein / Rieske domain | ||||||
Function / homology | Function and homology information : / dioxygenase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding Similarity search - Function | ||||||
Biological species | Comamonas testosteroni (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Mahto, J.K. / Kumar, P. | ||||||
Funding support | India, 1items
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Citation | Journal: J.Bacteriol. / Year: 2022 Title: Structural Insights into Dihydroxylation of Terephthalate, a Product of Polyethylene Terephthalate Degradation. Authors: Mahto, J.K. / Neetu, N. / Sharma, M. / Dubey, M. / Vellanki, B.P. / Kumar, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vju.cif.gz | 661.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vju.ent.gz | 544.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/7vju ftp://data.pdbj.org/pub/pdb/validation_reports/vj/7vju | HTTPS FTP |
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-Related structure data
Related structure data | 3gzxS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 46399.832 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Comamonas testosteroni (strain DSM 14576 / KF-1) (bacteria) Strain: DSM 14576 / KF-1 / Gene: CtesDRAFT_PD2130 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7WRJ9 #2: Protein | Mass: 17338.504 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Comamonas testosteroni (strain DSM 14576 / KF-1) (bacteria) Strain: DSM 14576 / KF-1 / Gene: CtesDRAFT_PD2129 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7WRJ8 |
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-Non-polymers , 7 types, 942 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / #6: Chemical | #7: Chemical | ChemComp-PO4 / #8: Chemical | ChemComp-PG4 / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.33 Å3/Da / Density % sol: 47.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2.4 M Ammonium phosphate dibasic, 0.1 M Tris pH 8.5, and 4% PEG 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.965 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→67.15 Å / Num. obs: 79803 / % possible obs: 96.7 % / Redundancy: 1.9 % / CC1/2: 0.984 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.27→2.32 Å / Num. unique obs: 4634 / CC1/2: 0.811 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3gzx Resolution: 2.27→67.15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.94 / SU B: 12.588 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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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: 153.8 Å2 / Biso mean: 51.09 Å2 / Biso min: 24.79 Å2
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Refinement step | Cycle: final / Resolution: 2.27→67.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.274→2.333 Å / Rfactor Rfree error: 0 / 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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