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- PDB-5u1e: Crystal structure of a methyltransferase involved in the biosynth... -

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Basic information

Entry
Database: PDB / ID: 5u1e
TitleCrystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with the kanamycin B
ComponentsPutative gentamicin methyltransferase
KeywordsTRANSFERASE / gentamicin methyltransferase SAH 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-9CS / S-ADENOSYL-L-HOMOCYSTEINE / N-3'' methyltransferase
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.213 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)38,2643
Polymers37,3961
Non-polymers8682
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.718, 68.168, 69.799
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-9CS / (1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE / Kanamycin B / Bekanamycin


Mass: 483.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37N5O10 / Comment: antibiotic*YM
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Magnesium chloride, tris pH 8, peg 3350, 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: Nov 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.213→48.77 Å / Num. obs: 30510 / % possible obs: 99.73 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.16

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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: 2.213→48.768 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26
RfactorNum. reflection% reflection
Rfree0.2468 3084 10.11 %
Rwork0.1888 --
obs0.1948 30510 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.16 Å2 / Biso mean: 36.9949 Å2 / Biso min: 17.17 Å2
Refinement stepCycle: final / Resolution: 2.213→48.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 59 126 2659
Biso mean--28.28 37.65 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082628
X-RAY DIFFRACTIONf_angle_d1.1863589
X-RAY DIFFRACTIONf_chiral_restr0.044406
X-RAY DIFFRACTIONf_plane_restr0.006476
X-RAY DIFFRACTIONf_dihedral_angle_d13.921969
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2131-2.24760.34231280.30141138126690
2.2476-2.28450.32331390.25991240137999
2.2845-2.32390.30221560.255312531409100
2.3239-2.36610.34641440.245312371381100
2.3661-2.41160.26221310.240412621393100
2.4116-2.46090.33341410.244512571398100
2.4609-2.51440.3161160.229312811397100
2.5144-2.57290.38991300.251512651395100
2.5729-2.63720.33321200.241712681388100
2.6372-2.70850.28981550.221312331388100
2.7085-2.78820.28161330.207412621395100
2.7882-2.87820.24921620.206512311393100
2.8782-2.9810.21781270.202312501377100
2.981-3.10040.22711580.194412411399100
3.1004-3.24140.26631500.198112381388100
3.2414-3.41230.24331400.179412621402100
3.4123-3.6260.26571550.172212291384100
3.626-3.90590.20921430.172212611404100
3.9059-4.29870.21881450.152212421387100
4.2987-4.92030.18771460.139112491395100
4.9203-6.1970.24051300.16812691399100
6.197-48.78030.19111350.160312581393100

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