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- PDB-5xj2: Structure of spRlmCD with U747 RNA -

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Basic information

Entry
Database: PDB / ID: 5xj2
TitleStructure of spRlmCD with U747 RNA
Components
  • RNA (5'-R(*GP*GP*CP*AP*CP*GP*UP*GP*CP*U)-3')
  • Uncharacterized RNA methyltransferase SP_1029
KeywordsTRANSFERASE/RNA / methyltransferase / 23S rRNA / U747 / 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 / RNA (> 10) / Uncharacterized RNA methyltransferase SP_1029
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4TIGR4 (bacteria)
Streptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsJiang, Y. / Gong, Q.
CitationJournal: PLoS ONE / Year: 2017
Title: Structural insights into substrate selectivity of ribosomal RNA methyltransferase RlmCD
Authors: Jiang, Y. / Li, F. / Wu, J. / Shi, Y. / Gong, Q.
History
DepositionApr 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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 / refine_hist / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)213,15613
Polymers211,3575
Non-polymers1,7998
Water27015
1
A: Uncharacterized RNA methyltransferase SP_1029
G: RNA (5'-R(*GP*GP*CP*AP*CP*GP*UP*GP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6484
Polymers57,1992
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized RNA methyltransferase SP_1029
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8363
Polymers51,3861
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized RNA methyltransferase SP_1029
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8363
Polymers51,3861
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Uncharacterized RNA methyltransferase SP_1029
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8363
Polymers51,3861
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.384, 94.916, 164.164
Angle α, β, γ (deg.)90.000, 95.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUAA1 - 4511 - 451
21METMETLEULEUBB1 - 4511 - 451
12LEULEULEULEUAA2 - 4512 - 451
22LEULEULEULEUCC2 - 4512 - 451
13LEULEUASPASPAA2 - 4522 - 452
23LEULEUASPASPDD2 - 4522 - 452
14LEULEULEULEUBB2 - 4512 - 451
24LEULEULEULEUCC2 - 4512 - 451
15LEULEULEULEUBB2 - 4512 - 451
25LEULEULEULEUDD2 - 4512 - 451
16LEULEULEULEUCC2 - 4512 - 451
26LEULEULEULEUDD2 - 4512 - 451

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Uncharacterized RNA methyltransferase SP_1029


Mass: 51386.047 Da / Num. of mol.: 4 / Fragment: UNP residues 1-454 / Mutation: E443Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4TIGR4 (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1029 / Plasmid: pET28aSUMO
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: Q97R12, Transferases; Transferring one-carbon groups; Methyltransferases
#2: RNA chain RNA (5'-R(*GP*GP*CP*AP*CP*GP*UP*GP*CP*U)-3')


Mass: 5812.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pneumoniae TIGR4 (bacteria)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM MES 0.1M ammonium sulfate 0.01 M magnesium chloride 20%PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: CCD / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 2.85→40 Å / Num. obs: 45742 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.366 / Rpim(I) all: 0.18 / Rrim(I) all: 0.409 / Χ2: 0.567 / Net I/σ(I): 2.9 / Num. measured all: 215130
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.94.10.99123260.6140.5251.1260.47899.9
2.9-2.954.31.06522370.6770.5511.2030.47799.7
2.95-3.014.40.99322810.6890.5071.1190.4899.6
3.01-3.074.30.98822530.7270.5051.1130.49499.7
3.07-3.144.30.89422650.7060.4581.0080.49299.7
3.14-3.214.50.86122750.7870.4330.9680.50399.8
3.21-3.294.70.75522850.8520.3710.8430.51799.9
3.29-3.384.50.62422700.860.3140.7010.522100
3.38-3.484.80.56922790.7820.2780.6340.587100
3.48-3.5950.47322690.9490.2250.5240.569100
3.59-3.7250.42722920.9460.2040.4740.61100
3.72-3.8750.40222710.9560.1920.4460.572100
3.87-4.0450.34522770.9660.1650.3830.64599.9
4.04-4.264.90.26623100.9730.1280.2960.60499.9
4.26-4.524.70.2122860.9660.1050.2350.657100
4.52-4.874.80.17922900.9810.0880.20.623100
4.87-5.364.80.19222870.9860.0930.2140.56299.7
5.36-6.135.20.21422970.9830.1010.2370.535100
6.13-7.724.90.17523130.9860.0840.1950.56899.7
7.72-404.70.08923790.9920.0430.0990.778100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UWV

1uwv


Resolution: 2.84→39.53 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.2175 / WRfactor Rwork: 0.1787 / FOM work R set: 0.8292 / SU B: 16.43 / SU ML: 0.307 / SU Rfree: 0.3937 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 1999 4.4 %RANDOM
Rwork0.1953 ---
obs0.1971 43704 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 154.4 Å2 / Biso mean: 29.664 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20.01 Å2
2---0.04 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.84→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14221 211 108 15 14555
Biso mean--46.33 6.57 -
Num. residues----1819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914822
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213916
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9620143
X-RAY DIFFRACTIONr_angle_other_deg1.015332257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33951805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75224.977663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.584152576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4931575
X-RAY DIFFRACTIONr_chiral_restr0.1050.22331
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116209
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022836
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A274940.1
12B274940.1
21A282700.09
22C282700.09
31A278900.11
32D278900.11
41B274600.11
42C274600.11
51B274520.11
52D274520.11
61C278540.11
62D278540.11
LS refinement shellResolution: 2.84→2.914 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 143 -
Rwork0.279 3115 -
all-3258 -
obs--95.8 %

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