+Open data
-Basic information
Entry | Database: PDB / ID: 8tdq | |||||||||
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Title | SFX-XFEL structure of CYP121 cocrystallized with substrate cYY | |||||||||
Components | Mycocyclosin synthase | |||||||||
Keywords | OXIDOREDUCTASE / SFX / room temperature / ES complex / P450 | |||||||||
Function / homology | Function and homology information mycocyclosin synthase / cyclase activity / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / carbon monoxide binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / oxidoreductase activity / iron ion binding / heme binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Nguyen, R.C. / Dasgupta, M. / Bhowmick, A. / Kern, J.F. / Liu, A. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121. Authors: Nguyen, R.C. / Davis, I. / Dasgupta, M. / Wang, Y. / Simon, P.S. / Butryn, A. / Makita, H. / Bogacz, I. / Dornevil, K. / Aller, P. / Bhowmick, A. / Chatterjee, R. / Kim, I.S. / Zhou, T. / ...Authors: Nguyen, R.C. / Davis, I. / Dasgupta, M. / Wang, Y. / Simon, P.S. / Butryn, A. / Makita, H. / Bogacz, I. / Dornevil, K. / Aller, P. / Bhowmick, A. / Chatterjee, R. / Kim, I.S. / Zhou, T. / Mendez, D. / Paley, D.W. / Fuller, F. / Alonso Mori, R. / Batyuk, A. / Sauter, N.K. / Brewster, A.S. / Orville, A.M. / Yachandra, V.K. / Yano, J. / Kern, J.F. / Liu, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tdq.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tdq.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 8tdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tdq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8tdq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8tdq_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 8tdq_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/8tdq ftp://data.pdbj.org/pub/pdb/validation_reports/td/8tdq | HTTPS FTP |
-Related structure data
Related structure data | 8tdpC 5wp2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43174.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: cyp121, Rv2276, MTCY339.34c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WPP7, mycocyclosin synthase | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-YTT / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2 M ammonium sulfate, 100 mM MES buffer pH 5.3 |
-Data collection
Diffraction | Mean temperature: 300 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.3045 Å |
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Dec 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3045 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→31.77 Å / Num. obs: 59457 / % possible obs: 99.94 % / Redundancy: 9.8 % / Biso Wilson estimate: 19.78 Å2 / CC1/2: 0.984 / R split: 0.143 / Net I/σ(I): 4.54 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 9.85 % / Mean I/σ(I) obs: 0.538 / Num. unique obs: 2912 / CC1/2: 0.14 / R split: 1.042 / % possible all: 99.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WP2 Resolution: 1.65→31.77 Å / SU ML: 0.2328 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.658 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→31.77 Å
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Refine LS restraints |
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LS refinement shell |
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