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- PDB-4x1o: Crystal structure of the 16S rRNA (adenine(1408)-N(1))-methyltran... -

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Basic information

Entry
Database: PDB / ID: 4x1o
TitleCrystal structure of the 16S rRNA (adenine(1408)-N(1))-methyltransferase 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: 1.7 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
DepositionNov 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Sep 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 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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)28,6271
Polymers28,6271
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.385, 66.113, 80.408
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: 28626.605 Da / Num. of mol.: 1
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.: 183 / 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: 1.97 Å3/Da / Density % sol: 37.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.03 M BisTris, 25.5 % PEG3350

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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: Oct 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 25598 / % possible obs: 99 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 32
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.2 / % possible all: 98.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MQ2

3mq2


Resolution: 1.7→37.495 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 1954 7.92 %
Rwork0.1774 --
obs0.1808 24665 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: 1 / Resolution: 1.7→37.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 0 183 1827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071677
X-RAY DIFFRACTIONf_angle_d1.0882295
X-RAY DIFFRACTIONf_dihedral_angle_d12.934611
X-RAY DIFFRACTIONf_chiral_restr0.042277
X-RAY DIFFRACTIONf_plane_restr0.005293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6996-1.74210.33881240.27051448X-RAY DIFFRACTION88
1.7421-1.78920.26411280.23011525X-RAY DIFFRACTION91
1.7892-1.84180.23061350.20331558X-RAY DIFFRACTION94
1.8418-1.90120.21581330.19121527X-RAY DIFFRACTION94
1.9012-1.96920.20061390.18481604X-RAY DIFFRACTION96
1.9692-2.0480.21311410.1791599X-RAY DIFFRACTION97
2.048-2.14120.24061410.17421609X-RAY DIFFRACTION97
2.1412-2.25410.2311400.17031650X-RAY DIFFRACTION99
2.2541-2.39530.20741420.16821659X-RAY DIFFRACTION98
2.3953-2.58020.21111410.17051649X-RAY DIFFRACTION99
2.5802-2.83980.23721450.18821699X-RAY DIFFRACTION99
2.8398-3.25050.2011470.17651694X-RAY DIFFRACTION100
3.2505-4.09450.21371470.16381714X-RAY DIFFRACTION100
4.0945-37.50390.22321510.17451776X-RAY DIFFRACTION97
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)
12.3166-0.11750.71382.8183-0.49842.70140.08760.1567-0.2119-0.47380.05510.06520.4449-0.0269-0.10760.29860.0087-0.02520.1576-0.01480.148345.436178.99712.5281
21.69421.23640.08082.0367-0.19091.08420.0273-0.0286-0.04090.0501-0.05380.05230.0806-0.00060.03520.10970.01750.00180.1281-0.02020.12743.420671.129732.3934
30.59620.8278-0.73641.7197-0.48121.3773-0.08570.25520.2612-0.13870.11020.24430.0372-0.2848-0.05710.1599-0.0066-0.01810.2552-0.00420.184535.701879.664729.3363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:97)
2X-RAY DIFFRACTION2(chain A and resid 98:184)
3X-RAY DIFFRACTION3(chain A and resid 185:226)

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