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- PDB-3p2e: Structure of an antibiotic related Methyltransferase -

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Basic information

Entry
Database: PDB / ID: 3p2e
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
Putative methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / 16S rRNA (adenine(1408)-N(1))-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsSivaraman, J. / Husain, N.
CitationJournal: Nucleic Acids Res. / Year: 2010
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 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,2724
Polymers51,5032
Non-polymers7692
Water8,809489
1
A: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1362
Polymers25,7511
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1362
Polymers25,7511
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.985, 64.985, 108.424
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: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 44.66 % / Mosaicity: 0.591 °

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1
DetectorDate: Jun 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 51311 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.066 / Χ2: 1.942 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.68-1.717.40.43325960.928100
1.71-1.747.40.38224910.967100
1.74-1.777.50.32325911.054100
1.77-1.817.50.30125691.05100
1.81-1.857.50.24525331.196100
1.85-1.897.50.22425711.31100
1.89-1.947.50.19625491.48100
1.94-1.997.50.15425601.661100
1.99-2.057.50.14125651.785100
2.05-2.127.50.12325612.02100
2.12-2.197.40.11125672.185100
2.19-2.287.50.10225372.409100
2.28-2.387.50.09325792.376100
2.38-2.517.50.08525792.448100
2.51-2.677.50.07825352.537100
2.67-2.877.50.07225982.719100
2.87-3.167.30.06825583.312100
3.16-3.627.30.0625833.469100
3.62-4.567.20.04325762.628100
4.56-507.50.0326131.38199.4

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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: 1.68→20 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflection
Rfree0.2322 4701 9.2 %
Rwork0.1966 --
obs-46629 91.2 %
Solvent computationBsol: 50.8829 Å2
Displacement parametersBiso max: 81.02 Å2 / Biso mean: 24.4563 Å2 / Biso min: 11.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.589 Å20 Å20 Å2
2--2.589 Å20 Å2
3----5.178 Å2
Refinement stepCycle: LAST / Resolution: 1.68→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 52 489 3755
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.225
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3sah.param

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