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- PDB-6sj8: Methyltransferase MtgA from Desulfitobacterium hafniense in compl... -

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Basic information

Entry
Database: PDB / ID: 6sj8
TitleMethyltransferase MtgA from Desulfitobacterium hafniense in complex with tetrahydrofolate
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 / Chem-44V / Tetrahydromethanopterin S-methyltransferase
Function and homology information
Biological speciesDesulfitobacterium hafniense DCB-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 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 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)67,98112
Polymers67,0172
Non-polymers96510
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-76 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.760, 83.850, 86.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 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 / Plasmid: pET-28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B8FUR2, tetrahydromethanopterin S-methyltransferase

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Non-polymers , 5 types, 588 molecules

#2: Chemical ChemComp-44V / (6S)-2-amino-6-methyl-5,6,7,8-tetrahydropteridin-4(3H)-one


Mass: 181.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
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: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 120092 / % possible obs: 99.1 % / Redundancy: 4.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.8
Reflection shellResolution: 1.35→1.45 Å / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 23073 / CC1/2: 0.74 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→15 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.089 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.048
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1573 5999 5 %RANDOM
Rwork0.1192 ---
obs0.1215 113987 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.66 Å2 / Biso mean: 19.422 Å2 / Biso min: 9.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å2-0 Å2
2---1.05 Å20 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 1.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 63 580 5351
Biso mean--28.41 36.07 -
Num. residues----610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0144873
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174568
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.6676595
X-RAY DIFFRACTIONr_angle_other_deg1.0731.65410660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76324.206214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6815820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.691514
X-RAY DIFFRACTIONr_chiral_restr0.080.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025402
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02908
X-RAY DIFFRACTIONr_rigid_bond_restr1.97539437
X-RAY DIFFRACTIONr_sphericity_free24.4195341
X-RAY DIFFRACTIONr_sphericity_bonded10.82859583
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 439 -
Rwork0.254 8335 -
all-8774 -
obs--99.34 %

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