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- PDB-5zth: Crystal structure of spRlmCD with U1939loop RNA at 3.24 angstrom -

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Basic information

Entry
Database: PDB / ID: 5zth
TitleCrystal structure of spRlmCD with U1939loop RNA at 3.24 angstrom
Components
  • RNA (5'-R(P*AP*AP*AP*(MUM)P*UP*CP*CP*U)-3')
  • Uncharacterized RNA methyltransferase SP_1029
KeywordsTRANSFERASE/RNA / methyltransferase / ribosome RNA / S.pneumoniae / intermediate / 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: 3.24 Å
AuthorsJiang, Y.Y. / Yu, H.L.
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
DepositionMay 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
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
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 1.3Oct 23, 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(P*AP*AP*AP*(MUM)P*UP*CP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1593
Polymers53,7752
Non-polymers3841
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-17 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.947, 95.531, 114.515
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: 51303.023 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(P*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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium dihydrogen Phosphate 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 3.24→50 Å / Num. obs: 8963 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.314 / Rpim(I) all: 0.106 / Rrim(I) all: 0.332 / Χ2: 0.488 / Net I/σ(I): 1.8
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
3.24-3.39.50.8634270.8080.2940.9130.455
3.3-3.369.80.7564300.8350.2530.7980.448
3.36-3.429.80.694510.8480.230.7280.473
3.42-3.499.70.6544320.8510.2190.6910.483
3.49-3.579.80.5824350.8830.1950.6140.489
3.57-3.6510.10.5084440.9280.1680.5360.489
3.65-3.749.90.4844360.9310.1610.5110.47
3.74-3.849.60.4584420.920.1550.4840.482
3.84-3.959.50.3824300.9340.1290.4040.485
3.95-4.088.80.3624330.9390.1290.3850.498
4.08-4.239.30.324520.9560.1110.3390.489
4.23-4.4100.2544510.9720.0840.2680.506
4.4-4.610.30.2334380.9810.0760.2450.487
4.6-4.84100.2224550.9860.0730.2340.495
4.84-5.14100.2224410.9830.0730.2340.487
5.14-5.549.50.2654520.9840.090.2810.454
5.54-6.098.70.2664610.9770.0950.2830.432
6.09-6.979.40.2484590.980.0850.2620.459
6.97-8.789.50.1454730.9940.0490.1530.472
8.78-508.10.0985210.9950.0350.1050.715

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJ1

5xj1


Resolution: 3.24→50 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.859 / SU B: 25.629 / SU ML: 0.433 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.59
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.268 459 5.1 %RANDOM
Rwork0.213 ---
obs0.2159 8466 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.77 Å2 / Biso mean: 45.903 Å2 / Biso min: 34.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0 Å2
2---0.04 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 3.24→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3608 164 26 0 3798
Biso mean--40.33 --
Num. residues----461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193883
X-RAY DIFFRACTIONr_bond_other_d0.0010.023632
X-RAY DIFFRACTIONr_angle_refined_deg1.0041.9515278
X-RAY DIFFRACTIONr_angle_other_deg0.82938443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3065452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00525.059170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46415683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2951519
X-RAY DIFFRACTIONr_chiral_restr0.0590.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02733
LS refinement shellResolution: 3.24→3.305 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.365 38 -
Rwork0.271 538 -
obs--90.28 %

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