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- PDB-5u1i: Crystal structure of a methyltransferase involved in the biosynth... -

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Basic information

Entry
Database: PDB / ID: 5u1i
TitleCrystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with the methylated Kanamycin B
ComponentsPutative gentamicin methyltransferase
KeywordsTRANSFERASE / Gentamicin Methyltransferase SAH Methylated kanamycin B
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: 1.932 Å
AuthorsBury, P. / Huang, F. / Leadlay, P. / Dias, M.V.B.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)15091888 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 28, 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

Downloads & links

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Assembly

Deposited unit
A: Putative gentamicin methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3744
Polymers37,4521
Non-polymers9223
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.045, 70.052, 86.008
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: 37451.898 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Calcium chloride, Hepes pH 8, Peg 6000

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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: Oct 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 1.932→43.896 Å / Num. obs: 23107 / % possible obs: 97.26 % / Redundancy: 2 % / Rmerge(I) obs: 0.023 / Net I/σ(I): 21.76

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U4T

5u4t


Resolution: 1.932→43.896 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.37
RfactorNum. reflection% reflection
Rfree0.2243 1168 5.06 %
Rwork0.1763 --
obs0.1787 23101 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.64 Å2 / Biso mean: 18.1266 Å2 / Biso min: 3.47 Å2
Refinement stepCycle: final / Resolution: 1.932→43.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 61 175 2617
Biso mean--12.96 22.85 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072544
X-RAY DIFFRACTIONf_angle_d0.9943479
X-RAY DIFFRACTIONf_chiral_restr0.054393
X-RAY DIFFRACTIONf_plane_restr0.006462
X-RAY DIFFRACTIONf_dihedral_angle_d11.6382084
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9324-2.02030.24771340.18792611274595
2.0203-2.12680.26121580.16822659281796
2.1268-2.26010.22551470.17082679282697
2.2601-2.43450.26251240.18762711283597
2.4345-2.67950.24461370.19412737287498
2.6795-3.06720.23411640.1962750291498
3.0672-3.86390.23111520.16982811296399
3.8639-43.90760.16971520.15952975312799

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