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- PDB-4oqe: Crystal structure of the tylM1 N,N-dimethyltransferase in complex... -

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Basic information

Entry
Database: PDB / ID: 4oqe
TitleCrystal structure of the tylM1 N,N-dimethyltransferase in complex with SAH and TDP-Fuc3NMe
ComponentsdTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
KeywordsTRANSFERASE / SAM methyltransferase / N-methyltransferase / S-adenosylmethionine
Function / homology
Function and homology information


dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase / S-adenosylmethionine-dependent methyltransferase activity / antibiotic biosynthetic process / methylation / protein homodimerization activity
Similarity search - Function
CAC2371-like domains / S-adenosyl-L-methionine-dependent methyltransferases / Methyltransferase domain 25 / Methyltransferase domain / Single Sheet / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
dTDP-3-N-methylamino-3,6-dideoxygalactose / S-ADENOSYL-L-HOMOCYSTEINE / dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
Similarity search - Component
Biological speciesStreptomyces fradiae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsThoden, J.B. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2014
Title: Production of a novel N-monomethylated dideoxysugar.
Authors: Thoden, J.B. / Holden, H.M.
History
DepositionFeb 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
B: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9676
Polymers57,0762
Non-polymers1,8924
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-17 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.885, 92.938, 77.879
Angle α, β, γ (deg.)90.00, 97.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase / Tylosin biosynthesis protein M1


Mass: 28537.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces fradiae (bacteria) / Gene: tylM1, tylMI / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P95748, dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-MMF / dTDP-3-N-methylamino-3,6-dideoxygalactose


Mass: 561.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H29N3O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 295 K / Method: batch / pH: 9
Details: 15-20% PEG3400, 200 mM sodium chloride, 5 mM S-adenosylhomocysteine, 10 mM TDP-3-N-methylamino-3,6-dideoxygalactose, pH 9, BATCH, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 10, 2013 / Details: Montel
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 24812 / % possible obs: 86.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 14
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2554 / Rsym value: 0.14 / % possible all: 71.8

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.7.0029refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OQD

4oqd


Resolution: 2.2→29.05 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.824 / SU ML: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.368 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27695 1251 5 %RANDOM
Rwork0.21533 ---
obs0.21864 24812 86.5 %-
all-24812 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.971 Å2
Baniso -1Baniso -2Baniso -3
1-5.44 Å20 Å24.22 Å2
2---4.11 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 124 212 3987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193880
X-RAY DIFFRACTIONr_bond_other_d0.0010.023549
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9775277
X-RAY DIFFRACTIONr_angle_other_deg0.8438133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.525478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31421.955179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.35415561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8631539
X-RAY DIFFRACTIONr_chiral_restr0.0880.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214388
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02941
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 63 -
Rwork0.343 1432 -
obs--71.39 %

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