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- PDB-7qbs: B12-dependent radical SAM methyltransferase, Mmp10 with [4Fe-4S] ... -

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Basic information

Entry
Database: PDB / ID: 7qbs
TitleB12-dependent radical SAM methyltransferase, Mmp10 with [4Fe-4S] cluster, cobalamin, S-adenosyl-L-methionine, and peptide bound.
Components
  • Methyl coenzyme M reductase-arginine methyltransferase Mmp10
  • Peptide from Methyl-coenzyme M reductase subunit alpha from Methanosarcina acetivorans
KeywordsMETAL BINDING PROTEIN / Radical SAM / B12 binding / methyltransferase / sp3 carbon methylation
Function / homology
Function and homology information


iron-sulfur cluster binding / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Radical SAM methyltransferase MA_4551-like / Putative radical SAM, N-terminal / Radical SAM-like domain / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
CO-METHYLCOBALAMIN / : / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Methyl coenzyme M reductase-arginine methyltransferase Mmp10
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.327 Å
AuthorsBernardo-Garcia, N. / Fyfe, C.D. / Chavas, L.M.G. / Legrand, P. / Benjdia, A. / Berteau, O.
Funding support France, 2items
OrganizationGrant numberCountry
European Research Council (ERC)617053 France
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0014 France
CitationJournal: Nature / Year: 2022
Title: Crystallographic snapshots of a B 12 -dependent radical SAM methyltransferase.
Authors: Fyfe, C.D. / Bernardo-Garcia, N. / Fradale, L. / Grimaldi, S. / Guillot, A. / Brewee, C. / Chavas, L.M.G. / Legrand, P. / Benjdia, A. / Berteau, O.
History
DepositionNov 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
B: Peptide from Methyl-coenzyme M reductase subunit alpha from Methanosarcina acetivorans
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6387
Polymers49,4652
Non-polymers2,1735
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.290, 119.290, 68.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Methyl coenzyme M reductase-arginine methyltransferase Mmp10


Mass: 47964.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Gene: mmp10, HA338_00275 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A832SFM5, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein/peptide Peptide from Methyl-coenzyme M reductase subunit alpha from Methanosarcina acetivorans


Mass: 1499.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Methanosarcina acetivorans (archaea)

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Non-polymers , 6 types, 215 molecules

#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-COB / CO-METHYLCOBALAMIN


Mass: 1344.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C63H91CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 23% (w/v) PEG8000, 100 mM Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857, 1.72200
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2020
RadiationMonochromator: Si(111) single-crystal channel-cut / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978571
21.7221
ReflectionResolution: 2.327→45 Å / Num. obs: 23924 / % possible obs: 99.6 % / Redundancy: 20.7 % / Biso Wilson estimate: 64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.045 / Net I/σ(I): 11.6
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 18.2 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 479 / CC1/2: 0.283 / % possible all: 95.2

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (16-JUL-2021)refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHARPphasing
SOLOMONphasing
RefinementMethod to determine structure: MAD / Resolution: 2.327→45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.264 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.211
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 1148 4.8 %RANDOM
Rwork0.1824 ---
obs0.1849 23924 99.7 %-
Displacement parametersBiso mean: 62.46 Å2
Baniso -1Baniso -2Baniso -3
1--2.033 Å20 Å20 Å2
2---2.033 Å20 Å2
3---4.0659 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.327→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 129 210 3577
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093441HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.244695HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1237SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes590HARMONIC5
X-RAY DIFFRACTIONt_it3441HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion16.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion458SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2861SEMIHARMONIC4
LS refinement shellResolution: 2.33→2.35 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4914 -4.38 %
Rwork0.3628 458 -
all0.3683 479 -
obs--86.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6982-0.03640.34611.57370.31322.149-0.01010.06750.05550.0906-0.00850.0208-0.21880.08740.0186-0.07360.0089-0.0348-0.1141-0.0021-0.0803-16.272430.437822.7796
22.0370.07021.40752.3774-0.14051.8374-0.06020.07490.177-0.4072-0.12480.3385-0.2449-0.10080.1850.00560.0845-0.059-0.0681-0.0673-0.0441-28.933230.4760.7911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|257 A|502 - A|503 }
2X-RAY DIFFRACTION2{ A|258 - A|501 A|504 B|* }

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