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- PDB-7suc: XFEL Serial Crystallography Reveals the Room Temperature Structur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7suc | ||||||||||||||||||||||||||||||
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Title | XFEL Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase | ||||||||||||||||||||||||||||||
![]() | (Methyl-coenzyme M reductase I subunit ...![]() | ||||||||||||||||||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
![]() | Ohmer, C.J. / Dasgupta, M. | ||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: XFEL serial crystallography reveals the room temperature structure of methyl-coenzyme M reductase. Authors: Ohmer, C.J. / Dasgupta, M. / Patwardhan, A. / Bogacz, I. / Kaminsky, C. / Doyle, M.D. / Chen, P.Y. / Keable, S.M. / Makita, H. / Simon, P.S. / Massad, R. / Fransson, T. / Chatterjee, R. / ...Authors: Ohmer, C.J. / Dasgupta, M. / Patwardhan, A. / Bogacz, I. / Kaminsky, C. / Doyle, M.D. / Chen, P.Y. / Keable, S.M. / Makita, H. / Simon, P.S. / Massad, R. / Fransson, T. / Chatterjee, R. / Bhowmick, A. / Paley, D.W. / Moriarty, N.W. / Brewster, A.S. / Gee, L.B. / Alonso-Mori, R. / Moss, F. / Fuller, F.D. / Batyuk, A. / Sauter, N.K. / Bergmann, U. / Drennan, C.L. / Yachandra, V.K. / Yano, J. / Kern, J.F. / Ragsdale, S.W. | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 765.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7sxmC ![]() 3m1vS 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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Unit cell |
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Components
-Methyl-coenzyme M reductase I subunit ... , 3 types, 6 molecules AaBbCc
#1: Protein | ![]() Mass: 60377.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg References: UniProt: P11558, ![]() #2: Protein | ![]() Mass: 47148.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg References: UniProt: P11560, ![]() #3: Protein | ![]() Mass: 28423.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg References: UniProt: P11562, ![]() |
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-Non-polymers , 7 types, 749 molecules ![](data/chem/img/MG.gif)
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![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F43.gif)
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![](data/chem/img/COM.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / #5: Chemical | ![]() #6: Chemical | ![]() #7: Chemical | #8: Chemical | ChemComp-ACT / | ![]() #9: Chemical | ChemComp-EDO / | ![]() #10: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.81 % Description: Pale yellow, Plate-like crystals ranging 20-60 microns in size |
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Crystal grow![]() | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.55 Details: 18% PEG 400, 150mM Mg Acetate, 100mM HEPES (pH 7.5) PH range: 7.5-8.0 / Temp details: Isotemp |
-Data collection
Diffraction | Mean temperature: 300 K / Ambient temp details: Isotemp / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Jul 11, 2020 / Frequency: 30 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→21.25 Å / Num. obs: 189345 / % possible obs: 99.91 % / Redundancy: 41.43 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 0.979 / R split: 0.515 / Net I/σ(I): 3.356 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 9.89 % / Mean I/σ(I) obs: 0.696 / Num. unique obs: 9505 / CC1/2: 0.379 / R split: 0.831 / % possible all: 99.82 |
Serial crystallography measurement | Collection time total: 0.68 hours / Focal spot size: 16 µm2 / Pulse duration: 30 fsec. / Pulse energy: 2200 µJ / Pulse photon energy: 9.5 keV / XFEL pulse repetition rate: 30 Hz |
Serial crystallography sample delivery | Description: Drop On Tape / Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: mother liquor Description: Crystal slurry is injected onto a kapton tape from an acoustic droplet injector (ADE). The drop travels on the tape towards the X-ray interaction point where it is hit by the XFEL beam. ...Description: Crystal slurry is injected onto a kapton tape from an acoustic droplet injector (ADE). The drop travels on the tape towards the X-ray interaction point where it is hit by the XFEL beam. This is the Drop-On-Tape (DOT) sample delivery system used by our team previously. |
Serial crystallography data reduction | Crystal hits: 24589 / Frames total: 73742 / Lattices indexed: 22706 / XFEL run numbers: 44-53 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3M1V Resolution: 1.9→21.25 Å / SU ML: 0.2017 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.6978 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: 30.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→21.25 Å
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Refine LS restraints |
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LS refinement shell |
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