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- PDB-5zq8: Crystal structure of spRlmCD with U747 stemloop RNA -

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Basic information

Entry
Database: PDB / ID: 5zq8
TitleCrystal structure of spRlmCD with U747 stemloop RNA
Components
  • RNA (5'-R(*CP*CP*GP*UP*(MUM)P*GP*AP*AP*AP*AP*GP*G)-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. / Nucleic acid-binding, OB-fold / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
NICKEL (II) ION / S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / 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: 2.18 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
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 / 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)111,4098
Polymers110,5234
Non-polymers8864
Water1,20767
1
B: Uncharacterized RNA methyltransferase SP_1029
C: RNA (5'-R(*CP*CP*GP*UP*(MUM)P*GP*AP*AP*AP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7054
Polymers55,2612
Non-polymers4432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-20 kcal/mol
Surface area20430 Å2
MethodPISA
2
A: Uncharacterized RNA methyltransferase SP_1029
D: RNA (5'-R(*CP*CP*GP*UP*(MUM)P*GP*AP*AP*AP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7054
Polymers55,2612
Non-polymers4432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-20 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.230, 62.259, 79.818
Angle α, β, γ (deg.)74.580, 85.470, 65.030
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 1 - 454 / Label seq-ID: 1 - 454

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein Uncharacterized RNA methyltransferase SP_1029


Mass: 51386.047 Da / Num. of mol.: 2 / 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(*CP*CP*GP*UP*(MUM)P*GP*AP*AP*AP*AP*GP*G)-3')


Mass: 3875.427 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium acetate, 0.1M sodium acetate, pH5.2, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.18→56.37 Å / Num. obs: 48209 / % possible obs: 87.8 % / Redundancy: 3.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.078 / Rrim(I) all: 0.152 / Net I/σ(I): 6.2 / Num. measured all: 176570
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.18-2.293.50.5511929954690.8910.3380.6472.267.9
6.88-56.373.60.081612217210.990.0490.09511.698.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJ1

5xj1


Resolution: 2.18→56.37 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.895 / SU B: 12.562 / SU ML: 0.297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.4 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3033 2293 4.8 %RANDOM
Rwork0.2454 ---
obs0.248 45786 87.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.26 Å2 / Biso mean: 39.567 Å2 / Biso min: 17.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.18→56.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6978 516 54 67 7615
Biso mean--56.84 31.83 -
Num. residues----932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0147741
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176755
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.63610619
X-RAY DIFFRACTIONr_angle_other_deg0.8621.69615736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8345906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90423.419351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.887151187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8991535
X-RAY DIFFRACTIONr_chiral_restr0.0640.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021409
Refine LS restraints NCS

Ens-ID: 1 / Number: 13362 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.176→2.232 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 205 -
Rwork0.366 3630 -
all-3835 -
obs--93.88 %

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