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

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Basic information

Entry
Database: PDB / ID: 4oqd
TitleCrystal structure of the tylM1 N,N-dimethyltransferase in complex with SAH and TDP-Qui3NMe2
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
TDP-3,6-dideoxy-3-N,N-dimethylglucose / 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 / SYNCHROTRON / PHASER / Resolution: 1.6 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
C: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
D: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,99112
Polymers114,1524
Non-polymers3,8398
Water11,656647
1
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)58,9956
Polymers57,0762
Non-polymers1,9204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-17 kcal/mol
Surface area19220 Å2
MethodPISA
2
C: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
D: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9956
Polymers57,0762
Non-polymers1,9204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-18 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.532, 92.050, 80.177
Angle α, β, γ (deg.)90.00, 106.10, 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.: 4
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.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-QDM / TDP-3,6-dideoxy-3-N,N-dimethylglucose


Mass: 575.398 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H31N3O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 293 K / Method: batch / pH: 9
Details: 15-20% PEG3400, 200 mM sodium chloride, 5 mM S-adenosylhomocysteine, 10 mM TDP-3-N,N-dimethylamino-3,6-dideoxyglucose, pH 9, batch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98789 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 12, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98789 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 123048 / Num. obs: 123048 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 43.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 4.3 / Num. unique all: 5330 / Rsym value: 0.176 / % possible all: 79.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: PHASER
Starting model: PDB ENTRY 3PFH

3pfh


Resolution: 1.6→41.24 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.292 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21602 6150 5 %RANDOM
Rwork0.18056 ---
obs0.18231 123048 91.42 %-
all-123048 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.063 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-2.21 Å2
2---0.02 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7317 0 252 647 8216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197797
X-RAY DIFFRACTIONr_bond_other_d00.027130
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.97910614
X-RAY DIFFRACTIONr_angle_other_deg0.874316351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8235966
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44822.011358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57151132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2491577
X-RAY DIFFRACTIONr_chiral_restr0.1140.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218811
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021878
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: 1.6→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 410 -
Rwork0.315 7292 -
obs--77.72 %

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