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- PDB-5zq1: Crystal structure of spRlmCD with U1939loop RNA at 3.10 angstrom -

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Basic information

Entry
Database: PDB / ID: 5zq1
TitleCrystal structure of spRlmCD with U1939loop RNA at 3.10 angstrom
Components
  • RNA (5'-R(*AP*AP*AP*(MUM)P*UP*CP*CP*U)-3')
  • Uncharacterized RNA methyltransferase SP_1029
KeywordsTRANSFERASE/RNA / methyltransferase / Ribosome / 23S RNA / Streptococcus pneumoniae / TRANSFERASE / TRANSFERASE-RNA complex
Function / homology
Function and homology information


rRNA (uridine-C5-)-methyltransferase activity / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases
Similarity search - Function
RNA methyltransferase TrmA, active site / RNA methyltransferase trmA family signature 1. / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / TRAM domain / TRAM domain / TRAM domain profile. ...RNA methyltransferase TrmA, active site / RNA methyltransferase trmA family signature 1. / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / TRAM domain / TRAM domain / TRAM domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / RNA / Uncharacterized RNA methyltransferase SP_1029
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
Streptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsYu, H.L. / Jiang, Y.Y.
CitationJournal: PLoS Pathog. / Year: 2018
Title: Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD
Authors: Jiang, Y. / Yu, H. / Li, F. / Cheng, L. / Zhu, L. / Shi, Y. / Gong, Q.
History
DepositionApr 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct.title
Revision 1.2Nov 22, 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
Revision 1.3Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized RNA methyltransferase SP_1029
B: RNA (5'-R(*AP*AP*AP*(MUM)P*UP*CP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0283
Polymers53,6432
Non-polymers3841
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-14 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.386, 96.097, 114.162
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized RNA methyltransferase SP_1029


Mass: 51171.832 Da / Num. of mol.: 1 / Mutation: E443Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1029
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q97R12, Transferases; Transferring one-carbon groups; Methyltransferases
#2: RNA chain RNA (5'-R(*AP*AP*AP*(MUM)P*UP*CP*CP*U)-3')


Mass: 2471.564 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pneumoniae TIGR4 (bacteria)
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES, pH 5.5, 0.15 M ammonium sulfate, 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 10101 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.059 / Rrim(I) all: 0.173 / Χ2: 0.912 / Net I/σ(I): 6.3 / Num. measured all: 84586
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.158.60.8445080.8010.3020.8990.909100
3.15-3.218.70.7254770.8580.2580.7710.968100
3.21-3.278.50.6614930.8630.2380.7041.012100
3.27-3.348.40.5354950.8960.1940.5710.943100
3.34-3.418.40.464960.9250.1680.4910.942100
3.41-3.498.30.3644940.9310.1330.3890.99999.6
3.49-3.587.50.3184870.9540.1220.3420.962100
3.58-3.6870.274960.950.1060.2910.94100
3.68-3.788.50.2564880.9640.0930.2731.039100
3.78-3.918.90.2285090.9770.0810.2430.932100
3.91-4.049.20.1854970.9820.0640.1960.956100
4.04-4.219.20.1554960.9880.0530.1640.866100
4.21-4.490.1175070.9920.0410.1240.856100
4.4-4.638.90.1055060.9930.0370.1120.83899.8
4.63-4.928.80.095100.9960.0320.0950.775100
4.92-5.38.50.0945070.9940.0340.10.747100
5.3-5.838.40.0985110.9940.0350.1050.70199.8
5.83-6.677.80.0935200.9920.0350.10.69599.4
6.67-8.397.50.0735290.990.0280.0780.74399.6
8.39-407.40.0865750.9860.0330.0921.44199

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJ1

5xj1


Resolution: 3.1→40 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.922 / SU B: 18.692 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 511 5.1 %RANDOM
Rwork0.1951 ---
obs0.1972 9422 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.55 Å2 / Biso mean: 64.795 Å2 / Biso min: 41.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 3.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 163 26 0 3789
Biso mean--59.53 --
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193874
X-RAY DIFFRACTIONr_bond_other_d0.0020.023621
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9515267
X-RAY DIFFRACTIONr_angle_other_deg0.90938417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1985451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77825.059170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14115680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4471519
X-RAY DIFFRACTIONr_chiral_restr0.070.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024128
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02732
LS refinement shellResolution: 3.1→3.181 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 32 -
Rwork0.289 677 -
all-709 -
obs--97.66 %

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