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- PDB-9ecn: M. acetivorans MCR containing a 2-methylglutamine modification -

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Basic information

Entry
Database: PDB / ID: 9ecn
TitleM. acetivorans MCR containing a 2-methylglutamine modification
Components(Methyl-coenzyme M reductase subunit ...) x 3
KeywordsTRANSFERASE / 2-methylglutamine / MCR / Methyl-coenzyme M reductase / post-translational modification
Function / homology
Function and homology information


coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / metal ion binding / cytoplasm
Similarity search - Function
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 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
Similarity search - Domain/homology
FACTOR 430 / DI(HYDROXYETHYL)ETHER / Chem-SHT / Coenzyme B / Methyl-coenzyme M reductase subunit beta / Methyl-coenzyme M reductase subunit gamma / Methyl-coenzyme M reductase subunit alpha
Similarity search - Component
Biological speciesMethanosarcina acetivorans C2A (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNair, S.K. / Borkar, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mbio / Year: 2025
Title: Genetic and biochemical characterization of a radical SAM enzyme required for post-translational glutamine methylation of methyl-coenzyme M reductase.
Authors: Rodriguez Carrero, R.J. / Lloyd, C.T. / Borkar, J. / Nath, S. / Mirica, L.M. / Nair, S. / Booker, S.J. / Metcalf, W.
History
DepositionNov 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-coenzyme M reductase subunit alpha
B: Methyl-coenzyme M reductase subunit alpha
C: Methyl-coenzyme M reductase subunit beta
D: Methyl-coenzyme M reductase subunit beta
E: Methyl-coenzyme M reductase subunit gamma
F: Methyl-coenzyme M reductase subunit gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,66211
Polymers284,9186
Non-polymers2,7445
Water24,9151383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54170 Å2
ΔGint-253 kcal/mol
Surface area57670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.470, 82.940, 122.470
Angle α, β, γ (deg.)90.00, 93.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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

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


Mass: 62208.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans C2A (archaea)
Gene: mcrA, MA_4546 / Production host: Methanosarcina acetivorans C2A (archaea)
References: UniProt: Q8THH1, coenzyme-B sulfoethylthiotransferase
#2: Protein Methyl-coenzyme M reductase subunit beta


Mass: 45174.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans C2A (archaea)
Gene: MA_4550 / Production host: Methanosarcina acetivorans C2A (archaea) / References: UniProt: Q8THG7
#3: Protein Methyl-coenzyme M reductase subunit gamma


Mass: 35076.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans C2A (archaea)
Gene: MA_4547 / Production host: Methanosarcina acetivorans C2A (archaea)
References: UniProt: Q8THH0, coenzyme-B sulfoethylthiotransferase

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Non-polymers , 5 types, 1388 molecules

#4: Chemical ChemComp-F43 / FACTOR 430


Mass: 906.580 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H51N6NiO13 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H22NO7PS / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SHT / O-PHOSPHONO-N-{(2E)-7-[(2-SULFOETHYL)DITHIO]HEPT-2-ENOYL}-L-THREONINE


Mass: 481.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H24NO10PS3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1383 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.83 %
Crystal growTemperature: 282.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% w/v PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 147424 / % possible obs: 99.5 % / Redundancy: 4.7 % / CC1/2: 0.994 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 2.89 / Num. unique obs: 20004 / CC1/2: 0.828 / Rrim(I) all: 0.673 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata processing
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.104 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19272 7370 5 %RANDOM
Rwork0.15213 ---
obs0.15416 140019 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20.17 Å2
2---2.16 Å20 Å2
3---0.91 Å2
Refinement stepCycle: 1 / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18834 0 180 1383 20397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01219398
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.81626267
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59852480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.1365128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.087103122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.22875
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214868
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1962.5519974
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7624.58312430
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9962.6949424
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.31826.632671
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 542 -
Rwork0.225 10292 -
obs--99.83 %

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