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- PDB-7yhe: Crystal structure of the triple mutant CmnC-L136Q,S138G,D249Y in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yhe | ||||||
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Title | Crystal structure of the triple mutant CmnC-L136Q,S138G,D249Y in complex with alpha-KG | ||||||
![]() | CmnC | ||||||
![]() | OXIDOREDUCTASE / hydroxylase / oxygenase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, S.J. / Hsiao, Y.H. / Lin, E.C. / Hsiao, P.Y. / Chang, C.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the alpha-ketoglutarate-dependent non-heme iron oxygenase CmnC in capreomycin biosynthesis and its engineering to catalyze hydroxylation of the substrate enantiomer. Authors: Hsiao, Y.H. / Huang, S.J. / Lin, E.C. / Hsiao, P.Y. / Toh, S.I. / Chen, I.H. / Xu, Z. / Lin, Y.P. / Liu, H.J. / Chang, C.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155 KB | Display | ![]() |
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PDB format | ![]() | 118.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 45.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vglC ![]() 7vgnC ![]() 7y5fC ![]() 7y5iC ![]() 7y5pC ![]() 7yw9C ![]() 2wboS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 39120.562 Da / Num. of mol.: 2 / Mutation: 136Q,S138G,D249Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cmnC / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PGE / | #4: Chemical | ChemComp-FE / | #5: 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: 2.63 Å3/Da / Density % sol: 53.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20 mM ammonium acetate, 24% v/v polyethylene glycol 400, 0.1 M sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→30 Å / Num. obs: 95108 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 24.05 |
Reflection shell | Resolution: 1.67→1.73 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 9456 / CC1/2: 0.757 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WBO Resolution: 1.67→27.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.674 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.087 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.59 Å2 / Biso mean: 16.668 Å2 / Biso min: 5.64 Å2
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Refinement step | Cycle: final / Resolution: 1.67→27.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.713 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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