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- PDB-6h40: High resolution structure of MeT1 from Mycobacterium hassiacum in... -

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Basic information

Entry
Database: PDB / ID: 6h40
TitleHigh resolution structure of MeT1 from Mycobacterium hassiacum in complex with 3-methoxy-1,2-propanediol.
ComponentsMethyltransferase domain protein
KeywordsTRANSFERASE / 3-O-methyltransferase
Function / homology
Function and homology information


MMP 1-O-methyltransferase / chondroitin sulfate biosynthetic process / 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
(2~{S})-3-methoxypropane-1,2-diol / S-ADENOSYL-L-HOMOCYSTEINE / MMP 1-O-methyltransferase
Similarity search - Component
Biological speciesMycolicibacterium hassiacum DSM 44199 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.053 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
DepositionJul 20, 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 1.2Jan 17, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,38810
Polymers25,4451
Non-polymers9439
Water5,044280
1
A: Methyltransferase domain protein
hetero molecules

A: Methyltransferase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,77720
Polymers50,8912
Non-polymers1,88618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+4/31
Buried area4920 Å2
ΔGint-42 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.134, 113.134, 41.107
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-840-

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.) Mycolicibacterium hassiacum DSM 44199 (bacteria)
Gene: C731_4163 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K5B7F3

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Non-polymers , 6 types, 289 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FW5 / (2~{S})-3-methoxypropane-1,2-diol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 293 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: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979295 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979295 Å / Relative weight: 1
ReflectionResolution: 1.053→97.977 Å / Num. obs: 138507 / % possible obs: 99.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.7
Reflection shellResolution: 1.053→1.071 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G7D

6g7d


Resolution: 1.053→48.988 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 9.72
RfactorNum. reflection% reflection
Rfree0.1197 6989 5.05 %
Rwork0.1081 --
obs0.1087 138501 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.053→48.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1703 0 60 280 2043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091871
X-RAY DIFFRACTIONf_angle_d1.1092550
X-RAY DIFFRACTIONf_dihedral_angle_d21.684670
X-RAY DIFFRACTIONf_chiral_restr0.091276
X-RAY DIFFRACTIONf_plane_restr0.007333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0533-1.06530.23742320.25184266X-RAY DIFFRACTION98
1.0653-1.07780.22362520.21334331X-RAY DIFFRACTION100
1.0778-1.0910.17121920.18834349X-RAY DIFFRACTION99
1.091-1.10480.18372450.16714363X-RAY DIFFRACTION100
1.1048-1.11930.18032080.15614402X-RAY DIFFRACTION100
1.1193-1.13460.16632230.14974370X-RAY DIFFRACTION100
1.1346-1.15090.15942380.13974331X-RAY DIFFRACTION100
1.1509-1.1680.13752380.13194404X-RAY DIFFRACTION100
1.168-1.18630.14022240.12484345X-RAY DIFFRACTION100
1.1863-1.20570.1222290.10844409X-RAY DIFFRACTION100
1.2057-1.22650.13632020.10434364X-RAY DIFFRACTION100
1.2265-1.24880.1082370.10414402X-RAY DIFFRACTION100
1.2488-1.27290.11262280.0964363X-RAY DIFFRACTION100
1.2729-1.29880.11082610.09194361X-RAY DIFFRACTION100
1.2988-1.32710.10142430.08994386X-RAY DIFFRACTION100
1.3271-1.3580.0982050.09284383X-RAY DIFFRACTION100
1.358-1.39190.10382290.09024399X-RAY DIFFRACTION100
1.3919-1.42960.10912220.08724414X-RAY DIFFRACTION100
1.4296-1.47160.09992090.07924424X-RAY DIFFRACTION100
1.4716-1.51910.08872290.07444388X-RAY DIFFRACTION100
1.5191-1.57340.09272200.07524403X-RAY DIFFRACTION100
1.5734-1.63640.09082650.084334X-RAY DIFFRACTION100
1.6364-1.71090.10112360.08634417X-RAY DIFFRACTION100
1.7109-1.80110.09612270.08914401X-RAY DIFFRACTION100
1.8011-1.9140.09992580.09394377X-RAY DIFFRACTION100
1.914-2.06170.10222650.09574410X-RAY DIFFRACTION100
2.0617-2.26920.11332050.0934401X-RAY DIFFRACTION99
2.2692-2.59760.10742790.1054354X-RAY DIFFRACTION99
2.5976-3.27260.14262460.12084451X-RAY DIFFRACTION100
3.2726-49.04150.13492420.12574510X-RAY DIFFRACTION98

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