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Yorodumi- PDB-7fjl: Crystal Structure of phthalate dioxygenase from Comamonas testost... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fjl | ||||||
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Title | Crystal Structure of phthalate dioxygenase from Comamonas testosteroni KF1 | ||||||
Components | Rieske (2Fe-2S) domain protein | ||||||
Keywords | OXIDOREDUCTASE / dioxygenase / bacterial protein / metalloprotein / Rieske domain | ||||||
Function / homology | Function and homology information 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Comamonas testosteroni (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Mahto, J.K. / Kumar, P. | ||||||
Funding support | India, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fjl.cif.gz | 1007 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fjl.ent.gz | 831 KB | Display | PDB format |
PDBx/mmJSON format | 7fjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fjl_validation.pdf.gz | 4.8 MB | Display | wwPDB validaton report |
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Full document | 7fjl_full_validation.pdf.gz | 4.8 MB | Display | |
Data in XML | 7fjl_validation.xml.gz | 121.1 KB | Display | |
Data in CIF | 7fjl_validation.cif.gz | 178.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/7fjl ftp://data.pdbj.org/pub/pdb/validation_reports/fj/7fjl | HTTPS FTP |
-Related structure data
Related structure data | 7fhrSC 7v25C 7v28C 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 , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 49168.383 Da / Num. of mol.: 6 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_PD2022 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7WQT1 |
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-Non-polymers , 6 types, 2662 molecules
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-FES / #4: Chemical | ChemComp-TLA / | #5: Chemical | ChemComp-SRT / #6: Chemical | ChemComp-EDO / #7: 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: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG4000, magnesium chloride, calcium chloride, sodium potassium tartrate |
-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 17, 2020 / Details: VERTICAL CRL |
Radiation | Monochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.965 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→158.59 Å / Num. obs: 191985 / % possible obs: 99 % / Redundancy: 1.8 % / CC1/2: 0.968 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 2.11→2.15 Å / Num. unique obs: 9011 / CC1/2: 0.828 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7FHR Resolution: 2.11→158.59 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.87 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.165 / 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: 174.94 Å2 / Biso mean: 37.679 Å2 / Biso min: 14.62 Å2
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Refinement step | Cycle: final / Resolution: 2.11→158.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.164 Å / Rfactor Rfree error: 0
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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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