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- PDB-5kyg: RAWV_CTD (Loop Structure) of 16S/23S 2'-O-methyltransferase TlyA -

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Basic information

Entry
Database: PDB / ID: 5kyg
TitleRAWV_CTD (Loop Structure) of 16S/23S 2'-O-methyltransferase TlyA
ComponentsCytotoxin / haemolysin homologue 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 / symbiont-mediated hemolysis of host erythrocyte / rRNA methyltransferase activity / rRNA methylation / methyltransferase activity / toxin activity / methylation / host cell plasma membrane / RNA binding ...16S rRNA (cytidine1409-2'-O)-methyltransferase / 23S rRNA (cytidine1920-2'-O)-methyltransferase / symbiont-mediated hemolysis of host erythrocyte / rRNA methyltransferase activity / rRNA methylation / methyltransferase activity / toxin activity / methylation / 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 profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily ...Haemolysin A /rRNA methyltransferase TlyA / : / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Vaccinia Virus protein VP39 / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cytotoxin / haemolysin homologue TlyA / 16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKuiper, E.G. / Conn, G.L.
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 21, 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 1.3Oct 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

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Assembly

Deposited unit
A: Cytotoxin / haemolysin homologue TlyA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7822
Polymers23,6901
Non-polymers921
Water81145
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint0 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.922, 70.922, 79.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsMonomer as determined by Gel-filtration.

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Components

#1: Protein Cytotoxin / haemolysin homologue TlyA


Mass: 23690.039 Da / Num. of mol.: 1 / Fragment: residues 15-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: tlyA, ERS007722_00402 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0U0QZA7, UniProt: P9WJ63*PLUS, 23S rRNA (cytidine1920-2'-O)-methyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 8% Tascimate pH 8.0, 20% PEG 3350

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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: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→53.04 Å / Num. obs: 16678 / % possible obs: 99.87 % / Redundancy: 12.8 % / CC1/2: 0.928 / Rmerge(I) obs: 0.121 / Net I/σ(I): 45.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 3.6 / CC1/2: 0.928 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EOV

5eov


Resolution: 1.9→53.04 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.28 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22399 1668 10 %RANDOM
Rwork0.17349 ---
obs0.17843 15009 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.628 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å2-0 Å2
2--0.17 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→53.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 6 45 1579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191563
X-RAY DIFFRACTIONr_bond_other_d0.0020.021542
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9612126
X-RAY DIFFRACTIONr_angle_other_deg0.93833518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6725206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01121.93562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80615235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6291517
X-RAY DIFFRACTIONr_chiral_restr0.0920.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211789
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6672.561827
X-RAY DIFFRACTIONr_mcbond_other2.6232.555826
X-RAY DIFFRACTIONr_mcangle_it3.6583.8221032
X-RAY DIFFRACTIONr_mcangle_other3.663.831033
X-RAY DIFFRACTIONr_scbond_it3.583.074736
X-RAY DIFFRACTIONr_scbond_other3.5623.075736
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4754.4161095
X-RAY DIFFRACTIONr_long_range_B_refined7.38831.3621642
X-RAY DIFFRACTIONr_long_range_B_other7.38631.3641642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.898→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 120 -
Rwork0.228 1073 -
obs--98.76 %
Refinement TLS params.Method: refined / Origin x: 23.037 Å / Origin y: -15.779 Å / Origin z: 5.052 Å
111213212223313233
T0.0353 Å2-0.0075 Å20.0136 Å2-0.0809 Å2-0.0216 Å2--0.0504 Å2
L2.9352 °20.3908 °2-0.8474 °2-1.8104 °20.2842 °2--2.1893 °2
S-0.0581 Å °0.3633 Å °-0.2622 Å °-0.2052 Å °0.0936 Å °-0.1569 Å °0.0724 Å °-0.0032 Å °-0.0355 Å °

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