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- PDB-6sjs: Methyltransferase of the MtgA N227A mutant from Desulfitobacteriu... -

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Basic information

Entry
Database: PDB / ID: 6sjs
TitleMethyltransferase of the MtgA N227A mutant from Desulfitobacterium hafniense in complex with methyl-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-THH / Tetrahydromethanopterin S-methyltransferase
Function and homology information
Biological speciesDesulfitobacterium hafniense DCB-2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)68,35611
Polymers66,9302
Non-polymers1,4259
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-59 kcal/mol
Surface area23160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.160, 84.260, 86.710
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: 33465.246 Da / Num. of mol.: 2 / Mutation: N227A
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
#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


Mass: 459.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N7O6 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
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: 1.8→30 Å / Num. obs: 51389 / % possible obs: 98.1 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.6
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7642 / CC1/2: 0.726

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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: 1.8→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.4 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.334 / ESU R Free: 0.128
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 2569 5 %RANDOM
Rwork0.1798 ---
obs0.1817 48810 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 60.05 Å2 / Biso mean: 22.296 Å2 / Biso min: 9.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å2-0 Å2-0 Å2
2---2.07 Å20 Å2
3---1.17 Å2
Refinement stepCycle: final / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4680 0 78 132 4890
Biso mean--37.4 28.2 -
Num. residues----608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0134854
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174605
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.6546576
X-RAY DIFFRACTIONr_angle_other_deg1.1841.58510703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8285606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35324.19210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55415816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8371514
X-RAY DIFFRACTIONr_chiral_restr0.0480.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02944
X-RAY DIFFRACTIONr_rigid_bond_restr0.47839459
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 187 -
Rwork0.25 3552 -
all-3739 -
obs--98.58 %
Refinement TLS params.

T12: 0.0001 Å2 / 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)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0084-0.0152-0.01650.1017-0.00020.0483-0.00130.001-0.00050.00040.00320.00630.0030.0023-0.00190.0004-0.00050.0121-0.00040.001223.5615-8.891363.5387
20.0060.00680.00680.1131-0.01070.04110.00040.0013-0.0017-0.00120.00330.0032-0.007-0.0012-0.00370.00190.00010.01260.00110.000914.889527.143660.5731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 306
2X-RAY DIFFRACTION2B3 - 901

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