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- PDB-7e8p: Crystal structure of a Flavin-dependent Monooxygenase HadA wild t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7e8p | |||||||||
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Title | Crystal structure of a Flavin-dependent Monooxygenase HadA wild type complexed with reduced FAD and 4-nitrophenol | |||||||||
![]() | Chlorophenol monooxygenase | |||||||||
![]() | OXIDOREDUCTASE / flavin monooxygenase / chlorophenol 4-monooxygenase | |||||||||
Function / homology | ![]() oxidoreductase activity, acting on the CH-CH group of donors / monooxygenase activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
Model details | Crystal structure of Flavin-dependent Monooxygenase HadA with FADH2 and 4-nitophenol | |||||||||
![]() | Pimviriyakul, P. / Jaruwat, A. / Chitnumsub, P. / Chaiyen, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into a flavin-dependent dehalogenase HadA explain catalysis and substrate inhibition via quadruple pi-stacking. Authors: Pimviriyakul, P. / Jaruwat, A. / Chitnumsub, P. / Chaiyen, 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 | ![]() | 411 KB | Display | ![]() |
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PDB format | ![]() | 332.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 75.5 KB | Display | |
Data in CIF | ![]() | 106.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7e8qC ![]() 6jhmS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 58623.164 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-517 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q53008, 4-hydroxyphenylacetate 3-monooxygenase #2: Chemical | ChemComp-FDA / #3: Chemical | #4: 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: 2.85 Å3/Da / Density % sol: 56.79 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 6.5 Details: 0.1 M Bis-Tris propane pH 6.5, 0.35 M sodium citrate tribasic dihydrate and 24% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Mar 13, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→20.74 Å / Num. obs: 118305 / % possible obs: 99.3 % / Redundancy: 5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.052 / Rrim(I) all: 0.122 / Net I/σ(I): 9.9 / Num. measured all: 586952 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JHM Resolution: 2.3→20.71 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.871 / SU B: 8.258 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.52 Å2 / Biso mean: 20.662 Å2 / Biso min: 2.02 Å2
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Refinement step | Cycle: final / Resolution: 2.3→20.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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