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- PDB-7suc: XFEL Serial Crystallography Reveals the Room Temperature Structur... -

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Basic information

Entry
Database: PDB / ID: 7suc
TitleXFEL Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase
Components(Methyl-coenzyme M reductase I subunit ...) x 3
KeywordsTRANSFERASE / Methyl-Coenzyme M Reductase (MCR) / Methanogens / METAL BINDING PROTEIN
Function / homology
Function and homology information


coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / metal ion binding / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / Methyl-coenzyme M reductase beta subunit, C-terminal domain ...Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / Methyl-coenzyme M reductase beta subunit, C-terminal domain / Methyl-coenzyme M reductase beta subunit, N-terminal domain / Methyl-coenzyme M reductase, alpha subunit, N-terminal / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Methyl-coenzyme M reductase, ferredoxin-like fold / Methyl-coenzyme M reductase, alpha subunit, C-terminal / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 2 / Methyl-coenzyme M reductase alpha subunit, C-terminal domain / Methyl-coenzyme M reductase alpha subunit, N-terminal domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 1-THIOETHANESULFONIC ACID / FACTOR 430 / Coenzyme B / Methyl-coenzyme M reductase I subunit alpha / Methyl-coenzyme M reductase I subunit beta / Methyl-coenzyme M reductase I subunit gamma
Similarity search - Component
Biological speciesMethanothermobacter marburgensis str. Marburg (archaea)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOhmer, C.J. / Dasgupta, M.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P41GM139687 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM55302 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110501 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126289 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117126 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169-01 United States
CitationJournal: J.Inorg.Biochem. / Year: 2022
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
DepositionNov 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-coenzyme M reductase I subunit alpha
B: Methyl-coenzyme M reductase I subunit beta
C: Methyl-coenzyme M reductase I subunit gamma
a: Methyl-coenzyme M reductase I subunit alpha
b: Methyl-coenzyme M reductase I subunit beta
c: Methyl-coenzyme M reductase I subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,97521
Polymers271,8996
Non-polymers3,07515
Water13,223734
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54190 Å2
ΔGint-279 kcal/mol
Surface area61070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.082, 119.777, 123.210
Angle α, β, γ (deg.)90.000, 91.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Methyl-coenzyme M reductase I subunit ... , 3 types, 6 molecules AaBbCc

#1: Protein Methyl-coenzyme M reductase I subunit alpha / MCR I alpha / Coenzyme-B sulfoethylthiotransferase alpha


Mass: 60377.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis str. Marburg (archaea)
Strain: ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg
References: UniProt: P11558, coenzyme-B sulfoethylthiotransferase
#2: Protein Methyl-coenzyme M reductase I subunit beta / MCR I beta / Coenzyme-B sulfoethylthiotransferase beta


Mass: 47148.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis str. Marburg (archaea)
Strain: ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg
References: UniProt: P11560, coenzyme-B sulfoethylthiotransferase
#3: Protein Methyl-coenzyme M reductase I subunit gamma / MCR I gamma / Coenzyme-B sulfoethylthiotransferase gamma


Mass: 28423.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter marburgensis str. Marburg (archaea)
Strain: ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg
References: UniProt: P11562, coenzyme-B sulfoethylthiotransferase

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Non-polymers , 7 types, 749 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-F43 / FACTOR 430


Mass: 906.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H51N6NiO13 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22NO7PS / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.81 %
Description: Pale yellow, Plate-like crystals ranging 20-60 microns in size
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 300 K / Ambient temp details: Isotemp / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.3007 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Jul 11, 2020 / Frequency: 30
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3007 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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 measurementCollection 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 deliveryDescription: Drop On Tape / Method: injection
Serial crystallography sample delivery injectionCarrier 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 reductionCrystal hits: 24589 / Frames total: 73742 / Lattices indexed: 22706 / XFEL run numbers: 44-53

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
cctbx.xfeldata reduction
cxi.mergedata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M1V

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
RfactorNum. reflection% reflection
Rfree0.1863 2008 1.06 %
Rwork0.1524 186898 -
obs0.1528 188906 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.52 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19098 0 195 734 20027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004420177
X-RAY DIFFRACTIONf_angle_d0.816927489
X-RAY DIFFRACTIONf_chiral_restr0.04643006
X-RAY DIFFRACTIONf_plane_restr0.00693644
X-RAY DIFFRACTIONf_dihedral_angle_d6.38262924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.29561440.284113114X-RAY DIFFRACTION98.57
1.95-20.28421400.257713335X-RAY DIFFRACTION99.85
2-2.060.26271420.231313305X-RAY DIFFRACTION99.99
2.06-2.130.24471390.214413376X-RAY DIFFRACTION100
2.13-2.20.23531460.195313298X-RAY DIFFRACTION100
2.2-2.290.21311460.185313333X-RAY DIFFRACTION100
2.29-2.390.22441420.177113348X-RAY DIFFRACTION100
2.39-2.520.23211470.170113370X-RAY DIFFRACTION100
2.52-2.680.22091460.171313332X-RAY DIFFRACTION100
2.68-2.880.21361420.162113350X-RAY DIFFRACTION100
2.88-3.170.18331460.149513392X-RAY DIFFRACTION100
3.17-3.630.16011410.128413424X-RAY DIFFRACTION100
3.63-4.570.14021420.103113431X-RAY DIFFRACTION99.98
4.57-21.250.12821450.11513490X-RAY DIFFRACTION99.44

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