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- PDB-5ks2: RAWV_CTD (Helix form) of 16S/23S 2'-O-methyltransferase TlyA -

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Basic information

Entry
Database: PDB / ID: 5ks2
TitleRAWV_CTD (Helix form) of 16S/23S 2'-O-methyltransferase TlyA
Components16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA
KeywordsTRANSFERASE / Methyltransferase / hemolysin / ribosome / antibiotic sensitivity
Function / homology
Function and homology information


16S rRNA (cytidine1409-2'-O)-methyltransferase / 23S rRNA (cytidine1920-2'-O)-methyltransferase / hemolysis by symbiont of host erythrocytes / rRNA methyltransferase activity / rRNA methylation / toxin activity / killing of cells of another organism / host cell plasma membrane / RNA binding / extracellular region ...16S rRNA (cytidine1409-2'-O)-methyltransferase / 23S rRNA (cytidine1920-2'-O)-methyltransferase / hemolysis by symbiont of host erythrocytes / rRNA methyltransferase activity / rRNA methylation / toxin activity / killing of cells of another organism / host cell plasma membrane / RNA binding / extracellular region / membrane / cytoplasm
Similarity search - Function
: / Haemolysin A /rRNA methyltransferase TlyA / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Vaccinia Virus protein VP39 / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / S4 RNA-binding domain profile. ...: / Haemolysin A /rRNA methyltransferase TlyA / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Vaccinia Virus protein VP39 / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / S4 RNA-binding domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsKuiper, E.G. / Conn, G.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI088025 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: A Novel Motif for S-Adenosyl-l-methionine Binding by the Ribosomal RNA Methyltransferase TlyA from Mycobacterium tuberculosis.
Authors: Witek, M.A. / Kuiper, E.G. / Minten, E. / Crispell, E.K. / Conn, G.L.
History
DepositionJul 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: 16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7252
Polymers23,6901
Non-polymers351
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.852, 67.852, 79.458
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsMonomer as determined by gel filtration

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Components

#1: Protein 16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA / 16S rRNA (cytidine1409-2'-O)-methyltransferase / 23S rRNA (cytidine1920-2'-O)-methyltransferase / ...16S rRNA (cytidine1409-2'-O)-methyltransferase / 23S rRNA (cytidine1920-2'-O)-methyltransferase / Hemolysin TlyA


Mass: 23690.039 Da / Num. of mol.: 1 / Fragment: residues 60-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: tlyA, Rv1694 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WJ63, 23S rRNA (cytidine1920-2'-O)-methyltransferase, 16S rRNA (cytidine1409-2'-O)-methyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.82 Å3/Da / Density % sol: 36.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.3 M Hepes pH 7.5 2.8M NaCl

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→51.6 Å / Num. obs: 10172 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.558 / Rmerge(I) obs: 0.319 / Net I/σ(I): 19.2
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 4.7 / CC1/2: 0.588 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EOV

5eov


Resolution: 2.18→51.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.378 / SU ML: 0.157 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.23 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 1018 10 %RANDOM
Rwork0.1926 ---
obs-10168 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 106.72 Å2 / Biso mean: 34.6 Å2 / Biso min: 18.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.39 Å2
Refinement stepCycle: final / Resolution: 2.18→51.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 1 71 1616
Biso mean--30.21 37.84 -
Num. residues----209
LS refinement shellResolution: 2.18→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 72 -
Rwork0.203 646 -
all-718 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 17.026 Å / Origin y: -11.176 Å / Origin z: 3.125 Å
111213212223313233
T0.028 Å20.0029 Å20.0139 Å2-0.0286 Å20.0018 Å2--0.02 Å2
L3.1575 °21.1544 °20.8726 °2-2.2086 °20.7915 °2--2.1451 °2
S-0.0527 Å °0.2395 Å °-0.063 Å °-0.147 Å °0.0239 Å °0.0147 Å °0.0708 Å °-0.0233 Å °0.0288 Å °
Refinement TLS groupSelection details: chain A

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