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

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Basic information

Entry
Database: PDB / ID: 7qbt
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 / IRON/SULFUR CLUSTER / Methyl coenzyme M reductase-arginine methyltransferase Mmp10
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
C: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
D: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,14824
Polymers191,8594
Non-polymers8,28920
Water22,8431268
1
A: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0376
Polymers47,9651
Non-polymers2,0725
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)50,0376
Polymers47,9651
Non-polymers2,0725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0376
Polymers47,9651
Non-polymers2,0725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0376
Polymers47,9651
Non-polymers2,0725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.064, 163.915, 77.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 47964.859 Da / Num. of mol.: 4
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 , 6 types, 1288 molecules

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


Mass: 351.640 Da / Num. of mol.: 4 / 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.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-COB / CO-METHYLCOBALAMIN


Mass: 1344.382 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C63H91CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1268 / 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: 2.59 Å3/Da / Density % sol: 52.57 %
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: 1.9→45.72 Å / Num. obs: 137077 / % possible obs: 99.8 % / Redundancy: 13.8 % / Biso Wilson estimate: 37.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.031 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2742 / CC1/2: 0.512 / Rpim(I) all: 0.847 / % possible all: 97.2

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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: 1.9→44.71 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.179 / SU Rfree Blow DPI: 0.15 / SU Rfree Cruickshank DPI: 0.147
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 6765 4.94 %RANDOM
Rwork0.203 ---
obs0.2026 137077 87 %-
Displacement parametersBiso mean: 44.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.3861 Å20 Å20 Å2
2--2.1619 Å20 Å2
3----1.7758 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 1.9→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12603 0 488 1268 14359
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913410HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1918316HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4810SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2308HARMONIC5
X-RAY DIFFRACTIONt_it13410HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion15.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1790SEMIHARMONIC5
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_contact11756SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.92 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2856 147 5.36 %
Rwork0.2971 2595 -
all0.2964 2742 -
obs--49.03 %
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)
10.30950.3527-0.25780.6307-0.02250.6493-0.0396-0.0251-0.0182-0.0721-0.00490.0723-0.00020.18440.0445-0.0407-0.04590.00020.0095-0.0002-0.0395-50.4545-18.2957-62.6015
20.1903-0.1828-0.4330.28010.20520.94520.11680.0108-0.0741-0.0067-0.12830.1151-0.12430.05180.01140.003-0.05540.0753-0.0213-0.052-0.0161-60.0937-8.3264-39.5519
30.57940.1478-0.37020.37140.56420.8144-0.04520.0567-0-0.00890.03760.04470.04210.09210.0075-0.0384-0.01610.0153-0.0168-0.0321-0.0294-50.0695-60.3469-20.8584
40.41270.0199-0.5980.98510.29920.720.0238-0.06850.01260.0978-0.03940.29230.02520.17010.0156-0.0266-0.00330.0673-0.0302-0.0760.0398-59.6334-52.35042.7935
51.414-0.0738-1.13350.2666-0.90371.61580.197-0.109-0.03290.0326-0.0302-0.05610.0159-0.0708-0.1668-0.0435-0.05340.04530.07590.0443-0.0894-23.2474-18.6201-18.0635
60.760.7449-0.47250.8415-0.77831.6197-0.01320.2927-0.04020.17330.0354-0.1710.135-0.2054-0.0222-0.14360.01580.04860.08340.1346-0.0373-14.9759-10.2442-42.2312
70.5381-0.2053-0.19750.40760.140.5821-0.0176-0.0190.00440.028-0.0248-0.10290.0348-0.16580.0424-0.05330.0333-0.01680.01350.0191-0.0375-22.3302-57.526-53.7899
80.1670.3329-0.14760.0975-0.31380.81040.01170.1212-0.04920.116-0.1025-0.0611-0.0975-0.05620.0908-0.02520.04180.030.03120.0914-0.0243-13.6204-47.0108-76.8905
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 }
5X-RAY DIFFRACTION5{ C|2 - C|257 C|502 - C|503 }
6X-RAY DIFFRACTION6{ C|258 - C|501 C|504 }
7X-RAY DIFFRACTION7{ D|1 - D|257 D|502 - D|503 }
8X-RAY DIFFRACTION8{ D|258 - D|501 D|504 }

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