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- PDB-3p2i: Structure of an antibiotic related Methyltransferase -

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Basic information

Entry
Database: PDB / ID: 3p2i
TitleStructure of an antibiotic related Methyltransferase
Components16S rRNA methylase
KeywordsTRANSFERASE / Methyltransferase / NpmA
Function / homology
Function and homology information


16S rRNA (adenine1408-N1)-methyltransferase / methyltransferase activity / methylation / response to antibiotic
Similarity search - Function
: / 16S rRNA (adenine(1408)-N(1))-methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
16S rRNA (adenine(1408)-N(1))-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSivaraman, J. / Husain, N.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit.
Authors: Husain, N. / Obranic, S. / Koscinski, L. / Seetharaman, J. / Babic, F. / Bujnicki, J.M. / Maravic-Vlahovicek, G. / Sivaraman, J.
History
DepositionOct 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S rRNA methylase
B: 16S rRNA methylase


Theoretical massNumber of molelcules
Total (without water)51,5032
Polymers51,5032
Non-polymers00
Water4,666259
1
A: 16S rRNA methylase


Theoretical massNumber of molelcules
Total (without water)25,7511
Polymers25,7511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 16S rRNA methylase


Theoretical massNumber of molelcules
Total (without water)25,7511
Polymers25,7511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.857, 64.857, 108.609
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein 16S rRNA methylase


Mass: 25751.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: npmA / Production host: Escherichia coli (E. coli) / References: UniProt: A8C927
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growpH: 5.5 / Details: pH 5.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.541 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19348 / % possible obs: 96.5 % / Redundancy: 8 % / Rmerge(I) obs: 0.102 / Χ2: 1.22 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3430.2567300.696176.3
2.34-2.385.20.2719710.667197.3
2.38-2.435.50.2599890.763198.2
2.43-2.485.90.2519800.811198.5
2.48-2.536.90.2299870.794199.5
2.53-2.596.20.21910141.052198.5
2.59-2.6660.2139451.333198.1
2.66-2.738.30.27310011.654199.1
2.73-2.817.30.1749911.293198.3
2.81-2.98.80.1579811.229199.3
2.9-39.50.1469991.286199.5
3-3.129.70.1259901.514198.6
3.12-3.269.60.1059951.11198.2
3.26-3.447.60.1089781.289196.6
3.44-3.656.10.1218821.064188.8
3.65-3.936.50.139240.574192
3.93-4.339.80.0859611.426195
4.33-4.9513.30.07310071.2161100
4.95-6.2411.50.0810042.417199.2
6.24-50110.07210190.564197.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PB3

3pb3


Resolution: 2.4→15 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflection
Rfree0.2656 1576 9 %
Rwork0.2052 --
obs-15777 90 %
Solvent computationBsol: 62.6972 Å2
Displacement parametersBiso max: 81.07 Å2 / Biso mean: 33.8772 Å2 / Biso min: 10.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.164 Å20 Å20 Å2
2--1.164 Å20 Å2
3----2.328 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 0 259 3443
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.156
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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