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

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Basic information

Entry
Database: PDB / ID: 7qbu
TitleB12-dependent radical SAM methyltransferase, Mmp10 with [4Fe-4S] cluster, cobalamin, and S-methyl-5'-thioadenosine bound.
ComponentsMethyl coenzyme M reductase-arginine methyltransferase Mmp10
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 / : / 5'-DEOXY-5'-METHYLTHIOADENOSINE / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / Methyl coenzyme M reductase-arginine methyltransferase Mmp10
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å
AuthorsFyfe, 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 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,28614
Polymers95,9302
Non-polymers4,35712
Water6,143341
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A: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1437
Polymers47,9651
Non-polymers2,1786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1437
Polymers47,9651
Non-polymers2,1786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.779, 79.493, 151.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 47964.859 Da / Num. of mol.: 2
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

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Non-polymers , 7 types, 353 molecules

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


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-COB / CO-METHYLCOBALAMIN


Mass: 1344.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H91CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (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 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2021
RadiationMonochromator: Si(111) single-crystal channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.298→44.84 Å / Num. obs: 37624 / % possible obs: 99.7 % / Redundancy: 12.8 % / Biso Wilson estimate: 51.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.034 / Net I/σ(I): 14.8
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 753 / CC1/2: 0.315 / Rpim(I) all: 0.907 / % possible all: 96.1

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (16-JUL-2021)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QBS

7qbs


Resolution: 2.298→44.84 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.416 / SU Rfree Blow DPI: 0.232 / SU Rfree Cruickshank DPI: 0.231
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1833 4.87 %RANDOM
Rwork0.191 ---
obs0.1927 37624 88.1 %-
Displacement parametersBiso mean: 50.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.4771 Å20 Å20 Å2
2--1.7597 Å20 Å2
3---0.7174 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.298→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6364 0 258 341 6963
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086769HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.219235HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2422SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1162HARMONIC5
X-RAY DIFFRACTIONt_it6769HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion17.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion899SEMIHARMONIC5
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_contact5609SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.33 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.269 -4.91 %
Rwork0.2956 716 -
all0.2942 753 -
obs--42.13 %
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)
10.806-0.37830.09681.0171-0.44920.7474-0.0475-0.22330.02580.01510.10250.0456-0.033-0.0835-0.055-0.11120.04830.0198-0.04450.0116-0.078-3.707916.721725.0253
21.2558-0.17-0.1561.4338-0.06071.02570.0788-0.06130.0026-0.2876-0.0483-0.0602-0.01340.1508-0.03050.00130.06330.023-0.0443-0.0052-0.061818.63936.707714.6049
31.14570.2811-0.22661.0709-0.39061.10780.14850.14520.12590.0797-0.2172-0.1431-0.05550.12110.0687-0.1259-0.05790.003-0.05320.0259-0.079740.597117.558652.3302
41.512-0.308-0.2591.4203-0.49851.37460.0986-0.00120.03170.04570.08020.0786-0.1019-0.197-0.1788-0.0901-0.04420.00510.01780.0196-0.056916.36310.6459.7638
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 }
3X-RAY DIFFRACTION3{ B|1 - B|257 B|502 - B|503 }
4X-RAY DIFFRACTION4{ B|258 - B|501 B|504 }

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