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- PDB-6sjk: Methyltransferase MtgA from Desulfitobacterium hafniense -

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Basic information

Entry
Database: PDB / ID: 6sjk
TitleMethyltransferase MtgA from Desulfitobacterium hafniense
ComponentsTetrahydromethanopterin S-methyltransferase
KeywordsTRANSFERASE / Anaerobic Bacteria / Glycine Betaine Metabolism / Methyl Transfer / Cobalamin / Tetrahydrofolate
Function / homologytetrahydromethanopterin S-methyltransferase / Tetrahydromethanopterin S-methyltransferase, subunit H/Methyltransferase Mtx, subunit H / Tetrahydromethanopterin S-methyltransferase MtrH subunit / Dihydropteroate synthase-like / one-carbon metabolic process / methyltransferase activity / methylation / Tetrahydromethanopterin S-methyltransferase
Function and homology information
Biological speciesDesulfitobacterium hafniense DCB-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 13, 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

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Assembly

Deposited unit
A: Tetrahydromethanopterin S-methyltransferase
B: Tetrahydromethanopterin S-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4777
Polymers67,0172
Non-polymers4605
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-38 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.110, 84.060, 86.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tetrahydromethanopterin S-methyltransferase


Mass: 33508.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense DCB-2 (bacteria)
Gene: Dhaf_4327 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B8FUR2, tetrahydromethanopterin S-methyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES, 27% 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: 1.85→30 Å / Num. obs: 46728 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.4
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6903 / CC1/2: 0.709

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Processing

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

6sj8


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.968 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.321 / ESU R Free: 0.13
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 2336 5 %RANDOM
Rwork0.1731 ---
obs0.1747 44379 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.24 Å2 / Biso mean: 26.833 Å2 / Biso min: 17.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---0.04 Å20 Å2
3----1.14 Å2
Refinement stepCycle: final / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 30 182 4898
Biso mean--45.55 34.37 -
Num. residues----608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134835
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174594
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.6416547
X-RAY DIFFRACTIONr_angle_other_deg1.1431.57510680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9255608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.724.206214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39615820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5421514
X-RAY DIFFRACTIONr_chiral_restr0.0490.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025368
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02946
X-RAY DIFFRACTIONr_rigid_bond_restr0.45739429
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 174 -
Rwork0.22 3299 -
all-3473 -
obs--99.37 %
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)
10.0305-0.0258-0.05670.3484-0.06660.1622-0.0066-0.0008-0.0041-0.00090.01810.01840.01210.0031-0.01150.0014-0.0014-0.00030.0096-0.00110.015223.6399-8.819463.6922
20.05210.00570.03660.28420.00740.11810.0077-0.00160.00130.00050.00010.0197-0.01870.0049-0.00790.0076-0.00210.00340.00450.0030.012714.798626.970460.6837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 306
2X-RAY DIFFRACTION2B3 - 306

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