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- PDB-3fzg: Structure of the 16S rRNA methylase ArmA -

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Basic information

Entry
Database: PDB / ID: 3fzg
TitleStructure of the 16S rRNA methylase ArmA
Components16S rRNA methylase
KeywordsTRANSFERASE / methyltransferase / Plasmid
Function / homology
Function and homology information


16S rRNA (guanine1405-N7)-methyltransferase / rRNA methyltransferase activity / response to antibiotic
Similarity search - Function
Ribosomal RNA aminoglycoside-resistance methyltransferase, Gram-negative bacteria / Ribosomal RNA aminoglycoside-resistance methyltransferase / Ribosomal RNA methyltransferase (FmrO) / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / 16S rRNA (guanine(1405)-N(7))-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsSchmitt, E. / Galimand, M. / Panvert, M. / Courvalin, P. / Mechulam, Y.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural bases for 16 S rRNA methylation catalyzed by ArmA and RmtB methyltransferases
Authors: Schmitt, E. / Galimand, M. / Panvert, M. / Courvalin, P. / Mechulam, Y.
History
DepositionJan 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7772
Polymers23,3791
Non-polymers3981
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.110, 90.080, 65.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

21A-374-

HOH

31A-439-

HOH

41A-514-

HOH

51A-518-

HOH

61A-552-

HOH

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Components

#1: Protein 16S rRNA methylase / ArmA / Aminoglycoside resistance 16S ribosomal RNA methylase


Mass: 23378.842 Da / Num. of mol.: 1 / Fragment: fragment 58-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: armA, pMUR050_016 / Plasmid: pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 rosetta / References: UniProt: Q6F5A0
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 50mM bis-tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2007 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→45.04 Å / Num. all: 15266 / Num. obs: 15048 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.022 / Rsym value: 0.022 / Net I/σ(I): 41.38
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.61 % / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 17.76 / Num. unique all: 1993 / Rsym value: 0.071 / % possible all: 98.1

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Processing

Software
NameVersionClassification
XDSdata scaling
SOLVEphasing
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2→45.04 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2063 897 -random
Rwork0.1899 ---
obs0.1899 15044 98.7 %-
all-15044 --
Displacement parametersBiso mean: 22.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.173 Å20 Å20 Å2
2---3.691 Å20 Å2
3---2.518 Å2
Refinement stepCycle: LAST / Resolution: 2→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1624 0 27 262 1913
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_bond_d0.0055
LS refinement shellResolution: 2→2.04 Å
RfactorNum. reflection
Rfree0.2665 57
Rwork0.195 -
obs-840

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