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- PDB-5bw5: Crystal structure of the 16S rRNA (adenine(1408)-N(1))-methyltran... -

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Basic information

Entry
Database: PDB / ID: 5bw5
TitleCrystal structure of the 16S rRNA (adenine(1408)-N(1))-methyltransferase D21A mutant from Catenulisporales acidiphilia
Components16S rRNA (adenine(1408)-N(1))-methyltransferase
KeywordsTRANSFERASE / methyltransferase / ribosome / aminoglycoside resistance
Function / homologyVaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / rRNA methyltransferase
Function and homology information
Biological speciesCatenulispora acidiphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWitek, M.A. / Conn, G.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI088025 United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Functional dichotomy in the 16S rRNA (m1A1408) methyltransferase family and control of catalytic activity via a novel tryptophan mediated loop reorganization.
Authors: Witek, M.A. / Conn, G.L.
History
DepositionJun 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 16S rRNA (adenine(1408)-N(1))-methyltransferase


Theoretical massNumber of molelcules
Total (without water)28,5831
Polymers28,5831
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.946, 66.663, 82.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 16S rRNA (adenine(1408)-N(1))-methyltransferase


Mass: 28582.598 Da / Num. of mol.: 1 / Mutation: D21A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catenulispora acidiphila (bacteria) / Strain: DSM 44928 / NRRL B-24433 / NBRC 102108 / JCM 14897 / Gene: Caci_9046 / Production host: Escherichia coli (E. coli) / References: UniProt: C7Q5P8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M Ammonium Acetate, 0.1 M Sodium Acetate trihydrate, pH 4.6, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8687 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.32 / Net I/σ(I): 15.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.4 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4X1O

4x1o


Resolution: 2.5→36.103 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2925 797 9.93 %
Rwork0.2393 --
obs0.2444 8023 92.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→36.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 0 35 1676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031674
X-RAY DIFFRACTIONf_angle_d0.7362291
X-RAY DIFFRACTIONf_dihedral_angle_d14.73609
X-RAY DIFFRACTIONf_chiral_restr0.026277
X-RAY DIFFRACTIONf_plane_restr0.004292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65040.33851010.2929976X-RAY DIFFRACTION76
2.6504-2.8550.38121260.28081118X-RAY DIFFRACTION88
2.855-3.14210.31321310.26331185X-RAY DIFFRACTION93
3.1421-3.59650.29591400.22451267X-RAY DIFFRACTION97
3.5965-4.52980.26261440.22031292X-RAY DIFFRACTION99
4.5298-36.10650.27821550.23431388X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8256-0.44310.44122.32661.07761.8488-0.0379-0.0894-0.11960.16360.04360.210.20260.1057-0.00010.3268-0.00860.00730.27010.04880.278-3.342613.6189-13.0987
21.3973-0.36940.2891.7973-0.32821.7562-0.02740.0509-0.1988-0.4256-0.04060.06370.16180.196-0.00130.3813-0.00010.04650.328-0.04470.3251-1.1325.7767-33.3827
30.5775-0.2078-0.57711.18530.66390.7758-0.0854-0.2610.2005-0.08540.1374-0.2891-0.04240.1643-0.00590.32410.0028-0.00430.45470.03590.43717.482213.652-29.1912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 8:97 )A8 - 97
2X-RAY DIFFRACTION2( CHAIN A AND RESID 98:188 )A98 - 188
3X-RAY DIFFRACTION3( CHAIN A AND RESID 189:226 )A189 - 226

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