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- PDB-3pb3: Structure of an Antibiotic Related Methyltransferase -

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Basic information

Entry
Database: PDB / ID: 3pb3
TitleStructure of an Antibiotic Related Methyltransferase
Components16S rRNA methylase
KeywordsTRANSFERASE / Antibiotic Resistance / 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 / SAD / Resolution: 1.9 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 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: 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_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)52,4164
Polymers51,6472
Non-polymers7692
Water5,783321
1
A: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2082
Polymers25,8241
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 16S rRNA methylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2082
Polymers25,8241
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-7 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.419, 64.419, 108.499
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: 25823.588 Da / Num. of mol.: 2 / Mutation: L31M, L90M, L128M, L196M
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


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


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.18 Å3/Da / Density % sol: 43.56 % / Mosaicity: 0.466 °

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C
DetectorDate: Sep 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 35024 / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.084 / Χ2: 3.644 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.9711.90.35334702.457100
1.97-2.0512.10.24534602.266100
2.05-2.1411.90.20635212.74100
2.14-2.2511.90.15534822.948100
2.25-2.3912.10.13935023.12100
2.39-2.5812.20.11335213.329100
2.58-2.8412.20.09734803.763100
2.84-3.2512.30.07635124.334100
3.25-4.0912.20.06335145.001100
4.09-50120.0635626.34999.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.111 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 1745 5 %RANDOM
Rwork0.2122 ---
obs0.2137 34747 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.81 Å2 / Biso mean: 22.1748 Å2 / Biso min: 6.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 52 321 3565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223312
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9774458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.775394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02124.4150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30315606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4431516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022446
X-RAY DIFFRACTIONr_mcbond_it0.5811.51982
X-RAY DIFFRACTIONr_mcangle_it1.13823196
X-RAY DIFFRACTIONr_scbond_it1.61831330
X-RAY DIFFRACTIONr_scangle_it2.7984.51262
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 106 -
Rwork0.246 2436 -
all-2542 -
obs--99.92 %

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