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- PDB-7sxm: Structure of Xenon-derivatized Methyl-Coenzyme M Reductase from M... -

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Basic information

Entry
Database: PDB / ID: 7sxm
TitleStructure of Xenon-derivatized Methyl-Coenzyme M Reductase from Methanothermobacter marburgensis
Components(Methyl-coenzyme M reductase I subunit ...) x 3
KeywordsTRANSFERASE / methyl-coenzyme M reductase / MCR / methanogens
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, alpha subunit, N-terminal subdomain 1 / 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, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit / Methyl-coenzyme M reductase beta subunit, C-terminal domain ...Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / 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, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit / 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 / XENON / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsChen, P.Y.-T. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 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 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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
D: Methyl-coenzyme M reductase I subunit alpha
E: Methyl-coenzyme M reductase I subunit beta
F: Methyl-coenzyme M reductase I subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,04127
Polymers271,8996
Non-polymers4,14221
Water15,097838
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.956, 115.741, 123.400
Angle α, β, γ (deg.)90.000, 92.525, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 258 or resid 260...
d_2ens_1(chain "D" and (resid 3 through 258 or resid 260...
d_1ens_2(chain "B" and (resid 2 through 364 or resid 373 through 418 or resid 420 through 443))
d_2ens_2(chain "E" and (resid 2 through 364 or resid 373 through 418 or resid 420 through 443))
d_1ens_3(chain "C" and (resid 2 through 50 or resid 52 through 247))
d_2ens_3(chain "F" and (resid 2 through 50 or resid 52 through 247))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPALAA1 - 256
d_12ens_1VALVALA259 - 268
d_13ens_1AGMILEA272 - 492
d_14ens_1GLNALAA494 - 550
d_15ens_1F43F43B
d_21ens_1ASPALAP1 - 256
d_22ens_1VALVALP259 - 268
d_23ens_1AGMILEP272 - 492
d_24ens_1GLNALAP496 - 552
d_25ens_1F43F43Q
d_11ens_2ALAHISK1 - 363
d_12ens_2GLYVALK380 - 425
d_13ens_2SERILEK429 - 452
d_21ens_2ALAHISU1 - 363
d_22ens_2GLYVALU380 - 425
d_23ens_2SERILEU429 - 452
d_11ens_3ALAPRON1 - 49
d_12ens_3VALASNN53 - 245
d_21ens_3ALAPROW1 - 49
d_22ens_3VALASNW51 - 243

NCS ensembles :
ID
ens_1
ens_2
ens_3

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Components

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

#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 , 8 types, 859 molecules

#4: Chemical ChemComp-F43 / FACTOR 430


Mass: 906.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H51N6NiO13
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22NO7PS
#8: Chemical ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O3S2
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Xe / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 838 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 uL of 24 mg/mL MCR was mixed with 1 uL of well solution (27% (w/v) PEG400, 0.18 M magnesium acetate, 0.25 M sodium chloride, and 0.10 M HEPES pH 7.5) to make a 2-uL sitting drop in a ...Details: 1 uL of 24 mg/mL MCR was mixed with 1 uL of well solution (27% (w/v) PEG400, 0.18 M magnesium acetate, 0.25 M sodium chloride, and 0.10 M HEPES pH 7.5) to make a 2-uL sitting drop in a sealed well with 30 uL well solution. Yellowish green rod MCR crystals grew in two to four hrs. The entire crystallization plate was shipped to Advanced Light Source Beamline 8.2.2 for Xe- pressurization and data collection. The crystals used to determine Xe-derivatized structure were transferred from the sitting drop into 2-5 uL of paraffin oil briefly and then sealed in a steel chamber pressurized with xenon at 180 psi for 10 mins. The Xe-derivatized crystals were flash-cooled in liquid nitrogen for data collection immediately.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.5498 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.503→69.633 Å / Num. obs: 151627 / % possible obs: 97.1 % / Redundancy: 3 % / Biso Wilson estimate: 35.38 Å2 / Rsym value: 0.086 / Net I/σ(I): 9.8
Reflection shellResolution: 2.503→2.59 Å / Num. unique obs: 14815 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M1V

3m1v


Resolution: 2.503→69.63 Å / SU ML: 0.2628 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5613
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.218 7573 5 %
Rwork0.1783 144002 -
obs0.1803 151575 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.81 Å2
Refinement stepCycle: LAST / Resolution: 2.503→69.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19038 0 207 838 20083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002219784
X-RAY DIFFRACTIONf_angle_d0.530726850
X-RAY DIFFRACTIONf_chiral_restr0.04062908
X-RAY DIFFRACTIONf_plane_restr0.00323554
X-RAY DIFFRACTIONf_dihedral_angle_d14.64867172
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.275814390883
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.31323338696
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.281198671524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.503-2.530.30242160.24414577X-RAY DIFFRACTION92.69
2.53-2.560.32052530.25234762X-RAY DIFFRACTION95.56
2.56-2.590.30492100.24714706X-RAY DIFFRACTION95.35
2.59-2.630.25842350.23714760X-RAY DIFFRACTION95.43
2.63-2.660.27492820.2264656X-RAY DIFFRACTION95.98
2.66-2.70.30262290.21664796X-RAY DIFFRACTION95.64
2.7-2.730.22962510.21494806X-RAY DIFFRACTION96.29
2.73-2.780.23742680.21094647X-RAY DIFFRACTION95.92
2.78-2.820.31172380.20264871X-RAY DIFFRACTION96.31
2.82-2.870.24632550.21414726X-RAY DIFFRACTION96.25
2.87-2.910.28612520.20544777X-RAY DIFFRACTION96.4
2.91-2.970.23962580.18964771X-RAY DIFFRACTION96.47
2.97-3.020.23612510.1954834X-RAY DIFFRACTION96.95
3.02-3.090.26052410.19544771X-RAY DIFFRACTION96.74
3.09-3.150.26012560.19524812X-RAY DIFFRACTION97.11
3.15-3.230.23222580.18614765X-RAY DIFFRACTION96.99
3.23-3.310.21662590.18254796X-RAY DIFFRACTION97.27
3.31-3.40.22082540.18184813X-RAY DIFFRACTION97.37
3.4-3.50.23072470.18274784X-RAY DIFFRACTION97.35
3.5-3.610.20912670.17094838X-RAY DIFFRACTION97.61
3.61-3.740.20312460.16424923X-RAY DIFFRACTION97.99
3.74-3.890.19562850.16114745X-RAY DIFFRACTION97.78
3.89-4.070.18452410.15734857X-RAY DIFFRACTION98
4.07-4.280.17942660.15314869X-RAY DIFFRACTION98.24
4.28-4.550.18522550.1514903X-RAY DIFFRACTION98.4
4.55-4.90.21782370.14614861X-RAY DIFFRACTION98.7
4.9-5.390.18432870.16494854X-RAY DIFFRACTION98.79
5.39-6.170.22172500.17824908X-RAY DIFFRACTION99.15
6.17-7.770.18672750.17434902X-RAY DIFFRACTION99.35
7.78-69.630.16372510.14714912X-RAY DIFFRACTION99.14

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