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- PDB-5tyq: Crystal structure of a holoenzyme methyltransferase involved in t... -

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Basic information

Entry
Database: PDB / ID: 5tyq
TitleCrystal structure of a holoenzyme methyltransferase involved in the biosynthesis of gentamicin
ComponentsPutative gentamicin methyltransferase
KeywordsTRANSFERASE / methyltransferase gentamicin biosynthesis SAM
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 / Homeobox domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / N-3'' methyltransferase
Similarity search - Component
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.163 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 21, 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 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)37,8043
Polymers37,3961
Non-polymers4092
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.692, 66.922, 68.849
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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: magnesium chloride, Tris, PEG 3350, PEG 400 / PH range: 7.0-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.163→47.903 Å / Num. obs: 16909 / % possible obs: 99.46 % / Redundancy: 11.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.175 / Net I/σ(I): 17.01

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.163→47.903 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.15
RfactorNum. reflection% reflection
Rfree0.216 813 4.81 %
Rwork0.1936 --
obs0.1969 16899 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.01 Å2 / Biso mean: 18.639 Å2 / Biso min: 2.32 Å2
Refinement stepCycle: final / Resolution: 2.163→47.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2354 0 27 110 2491
Biso mean--10.91 23.05 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082459
X-RAY DIFFRACTIONf_angle_d1.1793354
X-RAY DIFFRACTIONf_chiral_restr0.046371
X-RAY DIFFRACTIONf_plane_restr0.006450
X-RAY DIFFRACTIONf_dihedral_angle_d15.213918
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 (%)
2.1635-2.2990.35391290.25562563269297
2.299-2.47650.26371540.21826222776100
2.4765-2.72580.30951570.216826302787100
2.7258-3.12010.3065810.209827432824100
3.1201-3.93070.26341770.173126802857100
3.9307-47.91450.16741150.158828482963100

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