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- PDB-7qiu: YsgA 23s RNA methyltransferase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 7qiu
TitleYsgA 23s RNA methyltransferase from Bacillus subtilis
ComponentsrRNA methylase
KeywordsTRANSFERASE / 23s RNA methyltransferase
Function / homology
Function and homology information


RNA methyltransferase activity / RNA processing / RNA binding / cytoplasm
Similarity search - Function
RNA 2'-O ribose methyltransferase substrate binding / RNA 2-O ribose methyltransferase, substrate binding / RNA 2'-O ribose methyltransferase substrate binding / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
RNA methyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.877 Å
AuthorsLabar, G. / Van Elder, D. / Roovers, M. / Droogmans, L.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Other governmentFNRS BAG 20191372
Other governmentFNRS BAG 20171555 Belgium
CitationJournal: Rna / Year: 2022
Title: The Bacillus subtilis open reading frame ysgA encodes the SPOUT methyltransferase RlmP forming 2'- O -methylguanosine at position 2553 in the A-loop of 23S rRNA.
Authors: Roovers, M. / Labar, G. / Wolff, P. / Feller, A. / Van Elder, D. / Soin, R. / Gueydan, C. / Kruys, V. / Droogmans, L.
History
DepositionDec 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: rRNA methylase
B: rRNA methylase


Theoretical massNumber of molelcules
Total (without water)58,1982
Polymers58,1982
Non-polymers00
Water9,728540
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-9 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.880, 66.450, 129.600
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 rRNA methylase


Mass: 29099.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4122_3537, B4122_3803, B4417_0535 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A164ZSS2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 292 K / Method: microbatch / pH: 5.5 / Details: PEG3350 2%, MES 200mM pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980109 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980109 Å / Relative weight: 1
ReflectionResolution: 1.877→45.849 Å / Num. obs: 46483 / % possible obs: 99.7 % / Redundancy: 15.486 % / Biso Wilson estimate: 39.62 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.05 / Χ2: 0.903 / Net I/σ(I): 29.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.88-1.9315.2431.2552.2950486340833120.7741.29897.2
1.93-1.9815.9390.9033.4352948332833220.880.93399.8
1.98-2.0415.5880.6394.8550099321632140.9450.66199.9
2.04-2.114.7870.4516.6346343313531340.9660.467100
2.1-2.1715.9220.3498.8948275303230320.9820.36100
2.17-2.2416.1560.27711.2847869296429630.9890.286100
2.24-2.3315.9610.20115.1344963281728170.9940.207100
2.33-2.4215.1140.1518.8441532274827480.9960.155100
2.42-2.5315.7790.12222.9141498263026300.9980.127100
2.53-2.6516.480.09728.7941875254125410.9980.1100
2.65-2.816.3770.07735.8839206239423940.9990.079100
2.8-2.9716.0830.06342.836429226522650.9990.065100
2.97-3.1715.7980.0551.8334045215521550.9990.052100
3.17-3.4315.0140.04359.5130224201320130.9990.044100
3.43-3.7513.6680.03666.0925122183918380.9990.03799.9
3.75-4.215.2380.03274.67260121707170710.033100
4.2-4.8514.5390.02978.72218091500150010.03100
4.85-5.9414.0760.0374.62181581290129010.031100
5.94-8.414.9950.02679.76152801020101910.02799.9
8.4-45.84912.9810.02380.1376466005890.9990.02498.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5kzk

5kzk


Resolution: 1.877→45.849 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2074 2323 5 %
Rwork0.1821 44154 -
obs0.1833 46477 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.2 Å2 / Biso mean: 53.6323 Å2 / Biso min: 24.7 Å2
Refinement stepCycle: final / Resolution: 1.877→45.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 0 0 540 4327
Biso mean---63.37 -
Num. residues----500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8772-1.91550.35721310.3402250296
1.9155-1.95710.31821330.29252546100
1.9571-2.00260.30611340.27092545100
2.0026-2.05270.25551370.23652584100
2.0527-2.10820.23711350.23482571100
2.1082-2.17030.23611360.22332573100
2.1703-2.24030.27171350.23082592100
2.2403-2.32040.25171350.22292568100
2.3204-2.41330.26021360.22292568100
2.4133-2.52310.24891370.2172582100
2.5231-2.65610.26911360.20922623100
2.6561-2.82250.22151360.19482585100
2.8225-3.04040.23921370.19472608100
3.0404-3.34630.19631380.17932606100
3.3463-3.83030.16751400.15462648100
3.8303-4.82490.16571390.13292667100
4.8249-45.8490.18461480.17152786100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.23231.57591.39445.47540.84.12950.2535-0.1994-0.11350.8117-0.3188-0.19470.2380.12140.07710.4471-0.08910.00830.2852-0.03210.297810.884830.4552120.2147
28.8204-0.26950.29656.31532.478.16240.10880.16690.14060.6712-0.0807-0.83330.21610.4261-0.07480.4638-0.1101-0.06350.28530.07040.358916.678131.3545120.8561
32.25890.05373.66112.0651-1.68966.8088-0.0178-0.23590.09180.3254-0.01550.2269-0.0491-0.51120.04690.2475-0.00940.07070.3007-0.01190.2960.878335.612100.9013
42.95082.2362.36064.94370.85555.83510.3338-0.2567-0.04060.3143-0.13690.04960.3175-0.372-0.22680.2012-0.02290.04130.2930.0110.1859-0.86432.7181100.7332
52.91760.9694-4.02438.9688-4.74527.9130.25480.51750.2893-0.6341-0.13070.2737-0.1701-0.5999-0.16840.26180.0604-0.05810.43330.01640.3571-5.06140.711285.0657
66.45711.5205-1.68131.7663-1.36794.04920.0140.364-0.1847-0.423-0.00980.21920.3449-0.50390.01480.33760.016-0.03970.27150.00790.2491.671435.481984.0073
76.3096-3.49461.02178.96290.0322.8828-0.0424-0.30830.53320.04250.0579-0.4893-0.05250.0317-0.01930.41940.1554-0.02480.4701-0.07340.32735.397220.30881.3046
82.4211-4.3290.57194.6411-0.21391.54040.2850.0072-0.1057-0.5974-0.05430.09450.0621-0.1611-0.27770.44920.088-0.0330.4129-0.01770.379929.777819.943876.6058
92.3853-0.9211-1.1863.75911.11843.56090.1881-0.07460.22880.02080.0899-0.3159-0.28710.4692-0.27450.2963-0.00640.02130.3061-0.02080.289720.298946.107685.4095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 58 )A-2 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 91 )A59 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 127 )A92 - 127
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 174 )A128 - 174
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 204 )A175 - 204
6X-RAY DIFFRACTION6chain 'A' and (resid 205 through 248 )A205 - 248
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 42 )B0 - 42
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 104 )B43 - 104
9X-RAY DIFFRACTION9chain 'B' and (resid 105 through 248 )B105 - 248

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