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

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Basic information

Entry
Database: PDB / ID: 7qbv
TitleB12-dependent radical SAM methyltransferase, Mmp10 with [4Fe-4S] cluster, cobalamin, and S-adenosyl-L-homocysteine 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 / : / S-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER / Methyl coenzyme M reductase-arginine methyltransferase Mmp10
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 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)200,49724
Polymers191,8594
Non-polymers8,63720
Water1,13563
1
A: Methyl coenzyme M reductase-arginine methyltransferase Mmp10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1246
Polymers47,9651
Non-polymers2,1595
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)50,1246
Polymers47,9651
Non-polymers2,1595
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)50,1246
Polymers47,9651
Non-polymers2,1595
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)50,1246
Polymers47,9651
Non-polymers2,1595
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.498, 163.000, 77.328
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, 83 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
#4: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / 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
#6: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
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: 2.7→49.4 Å / Num. obs: 42049 / % possible obs: 99.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 68.25 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.07 / Net I/σ(I): 8.8
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 841 / CC1/2: 0.445 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (20-APR-2021)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QBS

7qbs


Resolution: 2.701→49.4 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.379
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 2062 4.9 %RANDOM
Rwork0.214 ---
obs0.2151 42049 76.7 %-
Displacement parametersBiso mean: 61.31 Å2
Baniso -1Baniso -2Baniso -3
1--3.8994 Å20 Å20 Å2
2--6.2029 Å20 Å2
3----2.3035 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.701→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12662 0 512 65 13239
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00613469HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0718390HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4830SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2314HARMONIC5
X-RAY DIFFRACTIONt_it13469HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1796SEMIHARMONIC5
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_contact10041SEMIHARMONIC4
LS refinement shellResolution: 2.701→2.77 Å
RfactorNum. reflection% reflection
Rfree0.2832 -4.64 %
Rwork0.3026 802 -
obs--21.27 %
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)
13.4722-0.85780.29040.83150.08923.73820.0257-0.0621-0.04090.0757-0.06750.1187-0.13790.09170.0418-0.24120.009-0.0237-0.1512-0.0264-0.154822.450257.42123.8753
22.12150.11930.93393.03870.49663.85740.23820.396-0.3184-0.3944-0.22190.39190.47890.0428-0.0164-0.13680.0663-0.06480.0545-0.1352-0.070713.787346.84280.779
32.79491.01810.67211.32520.09233.6202-0.0214-0.0986-0.0649-0.0232-0.0469-0.122-0.0207-0.23280.0683-0.2541-0.0351-0.0219-0.13310.05-0.177450.532418.263215.1063
42.2106-0.19961.04773.4897-0.5372.88450.3272-0.5116-0.46260.5442-0.1412-0.54420.54420.0879-0.18590.0481-0.0648-0.1520.12590.1436-0.027860.15188.214637.9289
54.17470.85861.07442.0373-0.40384.95870.05610.1476-0.0796-0.13390.0177-0.2674-0.0210.2577-0.0738-0.23920.0155-0.0583-0.10460.0753-0.100750.140960.0752-20.6208
63.0366-0.26131.05884.8568-0.98113.0891-0.0083-0.5437-0.10850.4821-0.0184-0.5442-0.04960.05810.0267-0.2043-0.0107-0.07050.05340.1411-0.077659.824552.17543.0176
75.197-0.27642.12611.75750.60046.30790.1916-0.31510.01250.0698-0.10050.2991-0.0615-0.3189-0.0911-0.1621-0.0908-0.03150.0253-0.075-0.114223.042118.5607-17.8929
83.98980.70422.30174.93151.31924.30940.12060.5442-0.336-0.5442-0.08070.5442-0.0642-0.0407-0.0399-0.11440.0817-0.10280.304-0.152-0.00214.79949.9962-41.9879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|257 A|502 - A|503 A|505 }
2X-RAY DIFFRACTION2{ A|258 - A|501 A|504 }
3X-RAY DIFFRACTION3{ B|1 - B|257 B|502 - B|503 B|505 }
4X-RAY DIFFRACTION4{ B|258 - B|501 B|504 }
5X-RAY DIFFRACTION5{ C|1 - C|257 C|502 - C|503 C|505 }
6X-RAY DIFFRACTION6{ C|258 - C|501 C|504 }
7X-RAY DIFFRACTION7{ D|1 - D|257 D|502 - D|503 D|505 }
8X-RAY DIFFRACTION8{ D|258 - D|501 D|504 }

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