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- PDB-5o95: Structure of the putative methyltransferase Lpg2936 from Legionel... -

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Basic information

Entry
Database: PDB / ID: 5o95
TitleStructure of the putative methyltransferase Lpg2936 from Legionella pneumophila
ComponentsRibosomal RNA small subunit methyltransferase E
KeywordsTRANSFERASE / RNA methyltransferase / RsmE-like
Function / homology
Function and homology information


16S rRNA (uracil1498-N3)-methyltransferase / methyltransferase activity / rRNA processing / methylation / cytoplasm
Similarity search - Function
Ribosomal RNA small subunit methyltransferase E, methyltransferase domain / Ribosomal RNA small subunit methyltransferase E, PUA-like domain / RNA methyltransferase PUA domain / Hypothetical PUA domain-like; domain 1 / Ribosomal RNA small subunit methyltransferase E / RNA methyltransferase domain / Ribosomal Protein L25; Chain P / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal ...Ribosomal RNA small subunit methyltransferase E, methyltransferase domain / Ribosomal RNA small subunit methyltransferase E, PUA-like domain / RNA methyltransferase PUA domain / Hypothetical PUA domain-like; domain 1 / Ribosomal RNA small subunit methyltransferase E / RNA methyltransferase domain / Ribosomal Protein L25; Chain P / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / PUA-like superfamily / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase E
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.491 Å
AuthorsPinotsis, N. / Waksman, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council321630 United Kingdom
CitationJournal: Protein Sci. / Year: 2017
Title: Crystal structure of the Legionella pneumophila Lpg2936 in complex with the cofactor S-adenosyl-L-methionine reveals novel insights into the mechanism of RsmE family methyltransferases.
Authors: Pinotsis, N. / Waksman, G.
History
DepositionJun 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal RNA small subunit methyltransferase E
B: Ribosomal RNA small subunit methyltransferase E
C: Ribosomal RNA small subunit methyltransferase E
D: Ribosomal RNA small subunit methyltransferase E


Theoretical massNumber of molelcules
Total (without water)109,3794
Polymers109,3794
Non-polymers00
Water21,6361201
1
A: Ribosomal RNA small subunit methyltransferase E
B: Ribosomal RNA small subunit methyltransferase E


Theoretical massNumber of molelcules
Total (without water)54,6892
Polymers54,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-6 kcal/mol
Surface area22920 Å2
MethodPISA
2
C: Ribosomal RNA small subunit methyltransferase E
D: Ribosomal RNA small subunit methyltransferase E


Theoretical massNumber of molelcules
Total (without water)54,6892
Polymers54,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-8 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.785, 144.777, 64.086
Angle α, β, γ (deg.)90.00, 100.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribosomal RNA small subunit methyltransferase E / Methyltransferase


Mass: 27344.740 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg2936 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5ZRE6, 16S rRNA (uracil1498-N3)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1201 / 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: 2.61 Å3/Da / Density % sol: 52.93 % / Description: beautiful crystals
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Optimised from morpheus screen: Mes/Imidazole pH 6.5 0.1 M EDO_Peg8K 27% Alcohols: 0.14 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.49→47.56 Å / Num. obs: 173267 / % possible obs: 95 % / Redundancy: 2.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Net I/σ(I): 10.6
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.1 / Num. unique all: 23778 / CC1/2: 0.725 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NXZ

1nxz


Resolution: 1.491→47.56 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9
RfactorNum. reflection% reflection
Rfree0.2095 8553 4.94 %
Rwork0.1791 --
obs0.1806 173103 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.491→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7625 0 0 1201 8826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078016
X-RAY DIFFRACTIONf_angle_d0.85710868
X-RAY DIFFRACTIONf_dihedral_angle_d17.863134
X-RAY DIFFRACTIONf_chiral_restr0.0811225
X-RAY DIFFRACTIONf_plane_restr0.0061429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.491-1.570.37232280.397623778X-RAY DIFFRACTION89.3
2.4211-2.54870.20282890.16125484X-RAY DIFFRACTION94
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)
10.53810.70870.44062.86821.43631.22580.0007-0.14460.10820.3913-0.14770.22170.0558-0.13180.1020.21630.0029-0.01840.156-0.00920.1913-5.741718.26477.4441
21.6102-0.13420.61281.84160.01182.06740.066-0.1257-0.05270.0587-0.01610.2930.1438-0.2315-0.04350.1111-0.0168-0.00780.1175-0.00010.1524-12.0158-3.5854-4.4441
30.81640.57720.24192.735-0.94630.94150.0554-0.12180.06060.1716-0.06660.0037-0.0343-0.02920.0090.13130.0208-0.00780.1466-0.02770.15276.982-16.064113.7975
42.3403-0.22710.66121.1073-0.43261.275-0.08460.180.2043-0.1734-0.0675-0.3148-0.07020.31950.10720.1261-0.00730.03210.18370.04030.208716.56781.1209-1.9396
51.09321.00430.15132.7035-0.35260.90870.02360.035-0.07130.0089-0.0705-0.18310.06590.12450.06350.15430.0346-0.01840.1463-0.01210.112938.2259-12.866340.8102
61.38260.28510.39731.40190.26522.45550.0377-0.2814-0.0780.2892-0.03440.15650.2061-0.2012-0.01840.1723-0.01770.03820.16620.00950.120420.3595-30.737647.2602
70.9809-1.14810.61992.9062-0.90920.84350.11260.1290.0444-0.1752-0.153-0.37240.13470.20130.04350.19380.0156-0.00640.15780.00290.190534.3457-47.624927.4385
81.7950.0380.58591.80050.20651.8245-0.06690.19910.0945-0.2458-0.005-0.105-0.09040.13830.06530.16080.004-0.00170.12410.0090.113123.4565-25.668119.2587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and ((resseq 4:153))
2X-RAY DIFFRACTION2chain 'D' and ((resseq 154:244))
3X-RAY DIFFRACTION3chain 'C' and ((resseq 4:153))
4X-RAY DIFFRACTION4chain 'C' and ((resseq 154:244))
5X-RAY DIFFRACTION5chain 'B' and ((resseq 1:153))
6X-RAY DIFFRACTION6chain 'B' and ((resseq 154:244))
7X-RAY DIFFRACTION7chain 'A' and ((resseq 3:153))
8X-RAY DIFFRACTION8chain 'A' and ((resseq 154:244))

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