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Yorodumi- PDB-6ydi: XFEL structure of the Soluble methane monooxygenase hydroxylase a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ydi | ||||||||||||||||||||||||||||||||||||||||||||||||
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Title | XFEL structure of the Soluble methane monooxygenase hydroxylase and regulatory subunit complex, from Methylosinus trichosporium OB3b, diferrous state | ||||||||||||||||||||||||||||||||||||||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / Ferritin superfamily / Soluble methane monooxygenase / Di-iron oxygen activation / Substrate oxidation. | ||||||||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information methane monooxygenase [NAD(P)H] activity / methane metabolic process / methane monooxygenase (soluble) / : / : / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / : / monooxygenase activity / one-carbon metabolic process / metal ion binding Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||||||||
Biological species | Methylosinus trichosporium OB3b (bacteria) | ||||||||||||||||||||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Authors | Srinivas, V. / Hogbom, M. | ||||||||||||||||||||||||||||||||||||||||||||||||
Funding support | Sweden, United States, United Kingdom, 15items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2020 Title: High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States. Authors: Srinivas, V. / Banerjee, R. / Lebrette, H. / Jones, J.C. / Aurelius, O. / Kim, I.S. / Pham, C.C. / Gul, S. / Sutherlin, K.D. / Bhowmick, A. / John, J. / Bozkurt, E. / Fransson, T. / Aller, P. ...Authors: Srinivas, V. / Banerjee, R. / Lebrette, H. / Jones, J.C. / Aurelius, O. / Kim, I.S. / Pham, C.C. / Gul, S. / Sutherlin, K.D. / Bhowmick, A. / John, J. / Bozkurt, E. / Fransson, T. / Aller, P. / Butryn, A. / Bogacz, I. / Simon, P. / Keable, S. / Britz, A. / Tono, K. / Kim, K.S. / Park, S.Y. / Lee, S.J. / Park, J. / Alonso-Mori, R. / Fuller, F.D. / Batyuk, A. / Brewster, A.S. / Bergmann, U. / Sauter, N.K. / Orville, A.M. / Yachandra, V.K. / Yano, J. / Lipscomb, J.D. / Kern, J. / Hogbom, M. | ||||||||||||||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ydi.cif.gz | 267.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ydi.ent.gz | 208.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ydi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ydi_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6ydi_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6ydi_validation.xml.gz | 45.9 KB | Display | |
Data in CIF | 6ydi_validation.cif.gz | 66.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/6ydi ftp://data.pdbj.org/pub/pdb/validation_reports/yd/6ydi | HTTPS FTP |
-Related structure data
Related structure data | 6yd0SC 6yduC 6yy3C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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
-Protein , 2 types, 2 molecules BF
#1: Protein | Mass: 45295.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methylosinus trichosporium OB3b (bacteria) References: UniProt: A0A2D2D5X7 |
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#3: Protein | Mass: 19444.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methylosinus trichosporium OB3b (bacteria) References: UniProt: A0A1A6FHH2, UniProt: A0A2D2D0T0*PLUS |
-Methane monooxygenase ... , 2 types, 2 molecules DG
#2: Protein | Mass: 60031.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Methylosinus trichosporium OB3b (bacteria) References: UniProt: P27353, methane monooxygenase (soluble) |
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#4: Protein | Mass: 14896.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria) Gene: mmoB / Production host: Escherichia coli (E. coli) / References: UniProt: P27356 |
-Non-polymers , 3 types, 472 molecules
#5: Chemical | ChemComp-GOL / | ||
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#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 3.11 Å3/Da / Density % sol: 60.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30 mM Sodium-Iodide, 30 mM Sodium-Bromide, 30 mM Sodium-Fluoride, 20% (v/v) Glycerol, 10% (w/v) PEG 4000, 100 mM HEPES/MOPS pH 7.5 10 mM Iron(III) chloride Temp details: Room temprature |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.30448 Å |
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Dec 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.30448 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→33.71 Å / Num. obs: 128981 / % possible obs: 99.98 % / Redundancy: 80.49 % / Biso Wilson estimate: 41.14 Å2 / CC1/2: 0.949 / Net I/σ(I): 27.519 |
Reflection shell | Resolution: 1.95→2.02 Å / Num. unique obs: 12716 / CC1/2: 0.175 / % possible all: 99.7 |
Serial crystallography measurement | Collection time total: 0.5 hours / Collimation: compound refractive lenses / Focal spot size: 4 µm2 / Pulse duration: 35 fsec. / Pulse energy: 4000 µJ / Pulse photon energy: 9.504 keV / XFEL pulse repetition rate: 20 Hz |
Serial crystallography sample delivery | Description: drop on tape combined with acustic droplet ejection Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: mother liquour / Description: acustic droplet ejection / Flow rate: 8 µL/min / Injector temperature: 298.15 K / Jet diameter: 230 µm / Power by: focused acoustic pulse |
Serial crystallography data reduction | Frames total: 36000 / Lattices indexed: 14980 / XFEL run numbers: 226-231 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YD0 Resolution: 1.95→33.71 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / Phase error: 24.03 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.73 Å2 / Biso mean: 45.7386 Å2 / Biso min: 27.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→33.71 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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