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- PDB-6g7d: Structure of MeT1 from Mycobacterium hassiacum in complex with SA... -

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Basic information

Entry
Database: PDB / ID: 6g7d
TitleStructure of MeT1 from Mycobacterium hassiacum in complex with SAM and glycerol.
ComponentsMethyltransferase domain protein
KeywordsTRANSFERASE / 3-O-methyltransferase
Function / homology
Function and homology information


MMP 1-O-methyltransferase / DIM/DIP cell wall layer assembly / methyltransferase activity / methylation / metal ion binding / plasma membrane
Similarity search - Function
Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / MMP 1-O-methyltransferase
Similarity search - Component
Biological speciesMycobacterium hassiacum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsPereira, P.J.B. / Ripoll-Rozada, J.
Funding support Portugal, 1items
OrganizationGrant numberCountry
SFRH/BPD/108004/2015 Portugal
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Biosynthesis of mycobacterial methylmannose polysaccharides requires a unique 1-O-methyltransferase specific for 3-O-methylated mannosides.
Authors: Ripoll-Rozada, J. / Costa, M. / Manso, J.A. / Maranha, A. / Miranda, V. / Sequeira, A. / Ventura, M.R. / Macedo-Ribeiro, S. / Pereira, P.J.B. / Empadinhas, N.
History
DepositionApr 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0987
Polymers25,4451
Non-polymers6536
Water5,134285
1
A: Methyltransferase domain protein
hetero molecules

A: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,19614
Polymers50,8912
Non-polymers1,30512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+4/31
Buried area4630 Å2
ΔGint-60 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.673, 113.673, 41.186
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methyltransferase domain protein


Mass: 25445.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria)
Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: C731_4163 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K5B7F3

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Non-polymers , 5 types, 291 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Details: This is a cofactor.
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 8.5, 0.2 M Magnesium chloride, 20% (wt/vol) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.35→49.222 Å / Num. obs: 67165 / % possible obs: 100 % / Redundancy: 18.5 % / Net I/σ(I): 9.7
Reflection shellResolution: 1.35→1.37 Å / Mean I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→49.222 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.96
RfactorNum. reflection% reflection
Rfree0.1715 3352 4.99 %
Rwork0.1414 --
obs0.1428 67115 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→49.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1729 0 15 285 2029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121885
X-RAY DIFFRACTIONf_angle_d1.062563
X-RAY DIFFRACTIONf_dihedral_angle_d21.961677
X-RAY DIFFRACTIONf_chiral_restr0.095275
X-RAY DIFFRACTIONf_plane_restr0.006341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36930.30531520.26632632X-RAY DIFFRACTION100
1.3693-1.38970.31071510.26482645X-RAY DIFFRACTION100
1.3897-1.41150.2681520.26182591X-RAY DIFFRACTION100
1.4115-1.43460.30531190.23852656X-RAY DIFFRACTION100
1.4346-1.45930.28941480.22472638X-RAY DIFFRACTION100
1.4593-1.48590.24441440.21052619X-RAY DIFFRACTION100
1.4859-1.51450.22841620.19182634X-RAY DIFFRACTION100
1.5145-1.54540.25031220.17312645X-RAY DIFFRACTION100
1.5454-1.5790.21841340.16732667X-RAY DIFFRACTION100
1.579-1.61570.20081550.16152624X-RAY DIFFRACTION100
1.6157-1.65610.22331330.15442651X-RAY DIFFRACTION100
1.6561-1.70090.16971330.15842632X-RAY DIFFRACTION100
1.7009-1.75090.21741460.14192661X-RAY DIFFRACTION100
1.7509-1.80750.1691470.12842632X-RAY DIFFRACTION100
1.8075-1.87210.15311340.11972679X-RAY DIFFRACTION100
1.8721-1.9470.15851030.11872663X-RAY DIFFRACTION100
1.947-2.03560.15661350.1072649X-RAY DIFFRACTION100
2.0356-2.1430.14871370.10822668X-RAY DIFFRACTION100
2.143-2.27720.13991320.10372682X-RAY DIFFRACTION100
2.2772-2.4530.15031460.11772648X-RAY DIFFRACTION100
2.453-2.69990.15961350.12942693X-RAY DIFFRACTION100
2.6999-3.09050.15861400.14142681X-RAY DIFFRACTION100
3.0905-3.89350.13911490.12822689X-RAY DIFFRACTION100
3.8935-49.25460.1521430.14132784X-RAY DIFFRACTION100

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