[English] 日本語
Yorodumi- PDB-7v28: Crystal Structure of phthalate dioxygenase in complex with tereph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v28 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of phthalate dioxygenase in complex with terephthalate | ||||||
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 Similarity search - Function | ||||||
Biological species | Comamonas testosteroni (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å | ||||||
Authors | Mahto, J.K. / Kumar, P. | ||||||
Funding support | India, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7v28.cif.gz | 483.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7v28.ent.gz | 397.3 KB | Display | PDB format |
PDBx/mmJSON format | 7v28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v28_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7v28_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 7v28_validation.xml.gz | 89.9 KB | Display | |
Data in CIF | 7v28_validation.cif.gz | 121.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/7v28 ftp://data.pdbj.org/pub/pdb/validation_reports/v2/7v28 | HTTPS FTP |
-Related structure data
Related structure data | 7fhrSC 7fjlC 7v25C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#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 #2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-FES / #4: Chemical | ChemComp-UB7 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.85 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
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: 3.07→160.43 Å / Num. obs: 63600 / % possible obs: 97.6 % / Redundancy: 1.9 % / CC1/2: 0.985 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3.07→3.14 Å / Num. unique obs: 4570 / CC1/2: 0.802 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7FHR Resolution: 3.07→160.43 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.832 / SU B: 23.517 / SU ML: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.477 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
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: 216.05 Å2 / Biso mean: 44.057 Å2 / Biso min: 0.5 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.07→160.43 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.07→3.147 Å / Rfactor Rfree error: 0
|