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- PDB-5u0t: Crystal structure of a methyltransferase involved in the biosynth... -

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Basic information

Entry
Database: PDB / ID: 5u0t
TitleCrystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-3-(methylamino)-alpha-D-glucopyranosyl]oxy}-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside
ComponentsPutative gentamicin methyltransferase
KeywordsTRANSFERASE / gentamicin methyltransferase
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / methylation / DNA binding / metal ion binding
Similarity search - Function
: / Methyltransferase small domain / Methyltransferase small domain / Methyltransferase domain / Homeobox domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-7QM / S-ADENOSYL-L-HOMOCYSTEINE / N-3'' methyltransferase
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.109 Å
AuthorsBury, P. / Huang, F. / Leadlay, P. / Dias, M.V.B.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2010/15971-3 Brazil
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Structural Basis of the Selectivity of GenN, an Aminoglycoside N-Methyltransferase Involved in Gentamicin Biosynthesis.
Authors: Bury, P.D.S. / Huang, F. / Li, S. / Sun, Y. / Leadlay, P.F. / Dias, M.V.B.
History
DepositionNov 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative gentamicin methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3024
Polymers37,3961
Non-polymers9063
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.815, 69.886, 84.700
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 Putative gentamicin methyltransferase


Mass: 37395.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: genN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2MG72
#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
#3: Chemical ChemComp-7QM / (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-3-(methylamino)-alpha-D-glucopyranosyl]oxy}-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside


Mass: 497.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H39N5O10
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: magnesium chloride, tris pH 8,0, peg 3350 and peg 400

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.109→43.58 Å / Num. obs: 17891 / % possible obs: 99.59 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.1074 / Net I/σ(I): 19.21

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U4T

5u4t


Resolution: 2.109→43.575 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.27
RfactorNum. reflection% reflection
Rfree0.2202 901 5.04 %
Rwork0.1539 --
obs0.1571 17891 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.65 Å2 / Biso mean: 25.1031 Å2 / Biso min: 7.92 Å2
Refinement stepCycle: final / Resolution: 2.109→43.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 60 200 2651
Biso mean--20.39 33.74 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082524
X-RAY DIFFRACTIONf_angle_d1.1453449
X-RAY DIFFRACTIONf_chiral_restr0.044392
X-RAY DIFFRACTIONf_plane_restr0.005456
X-RAY DIFFRACTIONf_dihedral_angle_d13.22919
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1092-2.24130.29111410.17422722286398
2.2413-2.41430.25211490.159128062955100
2.4143-2.65730.24481660.155627752941100
2.6573-3.04170.22871640.160228112975100
3.0417-3.83190.19431350.140328703005100
3.8319-43.58390.1971460.153730063152100

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