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- PDB-6sk4: Methyltransferase MtgA from Desulfitobacterium hafniense in compl... -

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Basic information

Entry
Database: PDB / ID: 6sk4
TitleMethyltransferase MtgA from Desulfitobacterium hafniense in complex with methyl-tetrahydrofolate (P21)
ComponentsMethylcorrinoid:tetrahydrofolate methyltransferase
KeywordsTRANSFERASE / Anaerobic Bacteria / Glycine Betaine Metabolism / Methyl Transfer / Cobalamin / Tetrahydrofolate
Function / homologyTetrahydromethanopterin S-methyltransferase, subunit H/Methyltransferase Mtx, subunit H / Tetrahydromethanopterin S-methyltransferase MtrH subunit / Dihydropteroate synthase-like / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / one-carbon metabolic process / methylation / Chem-THH / Methylcorrinoid:tetrahydrofolate methyltransferase
Function and homology information
Biological speciesDesulfitobacterium hafniense Y51 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBadmann, T. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1309 Germany
CitationJournal: Chembiochem / Year: 2020
Title: Structures in Tetrahydrofolate Methylation in Desulfitobacterial Glycine Betaine Metabolism at Atomic Resolution.
Authors: Badmann, T. / Groll, M.
History
DepositionAug 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Mar 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylcorrinoid:tetrahydrofolate methyltransferase
B: Methylcorrinoid:tetrahydrofolate methyltransferase
C: Methylcorrinoid:tetrahydrofolate methyltransferase
D: Methylcorrinoid:tetrahydrofolate methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,9639
Polymers134,0334
Non-polymers1,9305
Water7,242402
1
A: Methylcorrinoid:tetrahydrofolate methyltransferase
B: Methylcorrinoid:tetrahydrofolate methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0285
Polymers67,0172
Non-polymers1,0113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-37 kcal/mol
Surface area21770 Å2
MethodPISA
2
C: Methylcorrinoid:tetrahydrofolate methyltransferase
D: Methylcorrinoid:tetrahydrofolate methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9354
Polymers67,0172
Non-polymers9192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-36 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.400, 73.100, 89.760
Angle α, β, γ (deg.)90.000, 113.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Methylcorrinoid:tetrahydrofolate methyltransferase / Methylcobalamin:tetrahydrofolate methyltransferase / MethylCbl:THF methyltransferase


Mass: 33508.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense Y51 (bacteria)
Gene: mtgA, DSY3157 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q24SP6, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-THH / N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID / 5-METHYLTETRAHYDROFOLATE / Levomefolic acid


Mass: 459.456 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H25N7O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 35.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM TRIS, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 139692 / % possible obs: 97.2 % / Redundancy: 3.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Net I/σ(I): 8.1
Reflection shellResolution: 1.55→1.65 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 24053 / CC1/2: 0.823

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SJ8

6sj8


Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.723 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.109
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 6984 5 %RANDOM
Rwork0.2095 ---
obs0.2194 132691 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.31 Å2 / Biso mean: 21.902 Å2 / Biso min: 13.29 Å2
Baniso -1Baniso -2Baniso -3
1--3.13 Å20 Å21.15 Å2
2---1.75 Å20 Å2
3---2.83 Å2
Refinement stepCycle: final / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9228 0 138 402 9768
Biso mean--22.91 31.21 -
Num. residues----1197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0139570
X-RAY DIFFRACTIONr_bond_other_d0.0030.0179052
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.65912984
X-RAY DIFFRACTIONr_angle_other_deg1.2861.5921028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16851189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59624.111416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.928151597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9661528
X-RAY DIFFRACTIONr_chiral_restr0.0580.21272
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021882
X-RAY DIFFRACTIONr_rigid_bond_restr0.547318622
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 521 -
Rwork0.317 9896 -
all-10417 -
obs--98.39 %
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)
10.36010.10880.0430.1953-0.02280.0199-0.00280.01050.0098-0.0063-0.0053-0.01940.0111-0.0050.00810.11630.0018-0.00110.0747-0.00190.0039-2.8025-5.3815-0.7428
20.4869-0.0595-0.03810.0132-0.00680.05320.01130.02430.00310.0124-0.00120.003-0.0064-0.0082-0.01010.10710.00590.00120.0774-0.00260.0028-39.01610.93760.402
30.4980.0747-0.04960.0268-0.00490.05650.0124-0.02380.0265-0.01830.0045-0.00170.00960.0053-0.01690.109-0.0040.00310.0781-0.00060.0071-20.6499-18.313640.8205
40.3937-0.130.01120.24880.04180.0137-0.0039-0.00320.0104-0.004-0.00670.03980.00820.01160.01060.1111-0.0038-0.00610.07370.00610.0104-57.0624-24.320842.2346
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 901
2X-RAY DIFFRACTION2B3 - 901
3X-RAY DIFFRACTION3C3 - 901
4X-RAY DIFFRACTION4D3 - 901

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