+Open data
-Basic information
Entry | Database: PDB / ID: 5dqp | ||||||
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Title | EDTA monooxygenase (EmoA) from Chelativorans sp. BNC1 | ||||||
Components | EDTA monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / Monooxygenase / Bioremediation / EDTA degradation | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity Similarity search - Function | ||||||
Biological species | EDTA-degrading bacterium BNC1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.146 Å | ||||||
Authors | Jun, S.Y. / Youn, B. / Xun, L. / Kang, C. / Lewis, K.M. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2016 Title: Structural and biochemical characterization of EDTA monooxygenase and its physical interaction with a partner flavin reductase. Authors: Jun, S.Y. / Lewis, K.M. / Youn, B. / Xun, L. / Kang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dqp.cif.gz | 187.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dqp.ent.gz | 148.7 KB | Display | PDB format |
PDBx/mmJSON format | 5dqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/5dqp ftp://data.pdbj.org/pub/pdb/validation_reports/dq/5dqp | HTTPS FTP |
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-Related structure data
Related structure data | 1yw1S S: Starting model for refinement |
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Similar structure data |
-Links
-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: 47385.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) EDTA-degrading bacterium BNC1 (bacteria) Gene: emoA Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9F9T3 #2: Chemical | ChemComp-PE4 / | #3: Chemical | ChemComp-SO4 / | #4: 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: 2.64 Å3/Da / Density % sol: 53.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1M HEPES pH 7.5, 2% (w/v) PEG 400, and 1.75 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.146→45.02 Å / Num. obs: 56556 / % possible obs: 99.8 % / Redundancy: 10.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.191 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.146→2.18 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.194 / Mean I/σ(I) obs: 3.6 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YW1 Resolution: 2.146→45.021 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.146→45.021 Å
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Refine LS restraints |
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LS refinement shell |
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