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- PDB-5twk: Crystal Structure of RlmH in Complex with Sinefungin -

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Basic information

Entry
Database: PDB / ID: 5twk
TitleCrystal Structure of RlmH in Complex with Sinefungin
ComponentsRibosomal RNA large subunit methyltransferase H
KeywordsTRANSFERASE/ANTIBIOTIC / Sinefungin / RNA methyltransferase / SPOUT / pseudouridine / helix 69 / TRANSFERASE / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


23S rRNA (pseudouridine1915-N3)-methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase activity / rRNA base methylation / rRNA methylation / ribosome binding / protein homodimerization activity / cytoplasm
Similarity search - Function
RNA methyltransferase RlmH / Predicted SPOUT methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / Ribosomal RNA large subunit methyltransferase H / Ribosomal RNA large subunit methyltransferase H
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoh, C.S. / Madireddy, R. / Beane, T.J. / Zamore, P.D. / Korostelev, A.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM107465 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106105 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM62862 United States
CitationJournal: Sci Rep / Year: 2017
Title: Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine.
Authors: Koh, C.S. / Madireddy, R. / Beane, T.J. / Zamore, P.D. / Korostelev, A.A.
History
DepositionNov 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Ribosomal RNA large subunit methyltransferase H
D: Ribosomal RNA large subunit methyltransferase H
A: Ribosomal RNA large subunit methyltransferase H
B: Ribosomal RNA large subunit methyltransferase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6988
Polymers73,1724
Non-polymers1,5264
Water3,783210
1
C: Ribosomal RNA large subunit methyltransferase H
D: Ribosomal RNA large subunit methyltransferase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3494
Polymers36,5862
Non-polymers7632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-16 kcal/mol
Surface area14860 Å2
MethodPISA
2
A: Ribosomal RNA large subunit methyltransferase H
B: Ribosomal RNA large subunit methyltransferase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3494
Polymers36,5862
Non-polymers7632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-14 kcal/mol
Surface area14670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.370, 37.950, 121.820
Angle α, β, γ (deg.)90.00, 105.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribosomal RNA large subunit methyltransferase H / 23S rRNA (pseudouridine1915-N3)-methyltransferase / 23S rRNA m3Psi1915 methyltransferase / rRNA ...23S rRNA (pseudouridine1915-N3)-methyltransferase / 23S rRNA m3Psi1915 methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase RlmH


Mass: 18293.111 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rlmH / Production host: Escherichia coli (E. coli)
References: UniProt: B7MFQ9, UniProt: P0A8I8*PLUS, 23S rRNA (pseudouridine1915-N3)-methyltransferase
#2: Chemical
ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-bicine buffer (pH 8.5), 0.09 M NaF, 0.09 M NaBr, 0.09 M NaI, 20% v/v PEG 550 MME, 10% w/v PEG 20,000 in the presence of 2 mM Sinefungin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→39.1 Å / Num. obs: 34496 / % possible obs: 99.24 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06791 / Net I/σ(I): 17.66
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 1.95 / Num. unique obs: 3405 / % possible all: 93.52

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NS5

1ns5


Resolution: 2.1→39.084 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 1725 5 %
Rwork0.1833 --
obs0.1861 34486 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4960 0 108 210 5278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135204
X-RAY DIFFRACTIONf_angle_d1.2747080
X-RAY DIFFRACTIONf_dihedral_angle_d18.9732048
X-RAY DIFFRACTIONf_chiral_restr0.085760
X-RAY DIFFRACTIONf_plane_restr0.007888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16180.31981320.26432480X-RAY DIFFRACTION92
2.1618-2.23150.35751440.2442757X-RAY DIFFRACTION100
2.2315-2.31130.32721410.23682677X-RAY DIFFRACTION100
2.3113-2.40380.22431420.2122748X-RAY DIFFRACTION100
2.4038-2.51320.30331440.20632719X-RAY DIFFRACTION100
2.5132-2.64570.30271470.19682730X-RAY DIFFRACTION100
2.6457-2.81140.26031430.19282720X-RAY DIFFRACTION100
2.8114-3.02840.25291430.18792731X-RAY DIFFRACTION100
3.0284-3.3330.2311440.18542769X-RAY DIFFRACTION100
3.333-3.81490.2361440.17082773X-RAY DIFFRACTION100
3.8149-4.8050.17621500.14942794X-RAY DIFFRACTION100
4.805-39.09080.23051510.1782863X-RAY DIFFRACTION99
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)
12.9671-0.53780.81971.902-0.71823.41180.21871.2142-0.1102-0.3323-0.3811-0.20370.43961.07770.15110.55240.14510.00470.62790.02280.34051.93379.6399-55.3345
23.4416-1.05340.67172.9857-0.80364.7754-0.0038-0.3443-0.16270.13940.09750.1306-0.0075-0.4717-0.02730.2984-0.03030.00810.20620.05260.2439-10.756612.8687-33.2091
34.1951-0.2159-0.43732.89970.03682.70640.03380.63630.0113-0.2348-0.106-0.32570.10070.51170.0460.34950.03620.03730.4070.05560.282224.0968-6.3883-26.96
43.48770.18150.30162.55850.82964.2708-0.0539-0.73740.0230.0998-0.0549-0.11060.10810.12690.08410.2730.0268-0.01880.340.00920.243815.9401-7.2617-3.0538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid -1 through 155 )
2X-RAY DIFFRACTION2chain 'D' and (resid -1 through 155)
3X-RAY DIFFRACTION3chain 'A' and (resid -1 through 155 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 155 )

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