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- PDB-5zw4: Crystal structure of tRNA bound TrmR -

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Basic information

Entry
Database: PDB / ID: 5zw4
TitleCrystal structure of tRNA bound TrmR
Components
  • Putative O-methyltransferase YrrM
  • RNA (5'-R(*CP*CP*UP*GP*CP*UP*UP*UP*GP*CP*AP*CP*GP*CP*AP*GP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / transferase / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


tRNA (uridine) methyltransferase activity / O-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / magnesium ion binding
Similarity search - Function
tRNA 5-hydroxyuridine methyltransferase / O-methyltransferase / Class I-like SAM-dependent O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / S-ADENOSYLMETHIONINE / RNA / RNA (> 10) / tRNA 5-hydroxyuridine methyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Bacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKim, J. / Ryu, H. / Almo, S.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2016R1D1A1B03930716 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine.
Authors: Ryu, H. / Grove, T.L. / Almo, S.C. / Kim, J.
History
DepositionMay 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.formula_weight
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative O-methyltransferase YrrM
D: RNA (5'-R(*CP*CP*UP*GP*CP*UP*UP*UP*GP*CP*AP*CP*GP*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9304
Polymers31,4372
Non-polymers4932
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.982, 64.982, 126.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative O-methyltransferase YrrM


Mass: 26041.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: yrrM, BSU27360 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O32036, Transferases; Transferring one-carbon groups; Methyltransferases
#2: RNA chain RNA (5'-R(*CP*CP*UP*GP*CP*UP*UP*UP*GP*CP*AP*CP*GP*CP*AP*GP*G)-3')


Mass: 5395.237 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4 M Ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50.01 Å / Num. obs: 32851 / % possible obs: 94.1 % / Redundancy: 17.5 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.024 / Rrim(I) all: 0.093 / Χ2: 1.718 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.7-1.739.514000.4490.6771.35781.4
1.73-1.7610.514550.5560.51.39883.5
1.76-1.7911.315580.6990.411.41892.2
1.79-1.8312.416430.7410.3291.4596.1
1.83-1.8713.917310.8880.2851.51199.8
1.87-1.9113.117150.9380.7942.16999.9
1.91-1.9615.317040.9710.2192.56299.80.8050.836
1.96-2.0221.617410.9840.1111.7041000.5090.521
2.02-2.0721.717220.990.0711.6641000.3250.333
2.07-2.1421.717150.9930.0591.6881000.270.277
2.14-2.2220.917320.9940.061.8791000.2690.276
2.22-2.3112.49590.9760.0872.31555.50.3110.325
2.31-2.4121.517540.9970.0341.7721000.1550.159
2.41-2.5421.417310.9970.0291.8021000.1310.134
2.54-2.721.217710.9970.0251.821000.1120.114
2.7-2.912117370.9980.0211.81000.0950.098
2.91-3.220.417650.9980.0191.6031000.0840.086
3.2-3.661915900.9980.0171.4789.20.0730.075
3.66-4.6118.315580.9990.0151.46786.40.0640.066
4.61-501718700.9970.0161.41597.30.0650.067

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GPY

2gpy


Resolution: 1.7→50.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.243 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.11
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 1613 5.1 %RANDOM
Rwork0.1928 ---
obs0.1943 30082 90.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 208.14 Å2 / Biso mean: 44.255 Å2 / Biso min: 18.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 1.7→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 317 32 162 2266
Biso mean--34.87 45.99 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0182223
X-RAY DIFFRACTIONr_bond_other_d00.021904
X-RAY DIFFRACTIONr_angle_refined_deg2.0031.8593076
X-RAY DIFFRACTIONr_angle_other_deg0.95534434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5616.254295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94724.02292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4215332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1051514
X-RAY DIFFRACTIONr_chiral_restr0.160.202340
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022223
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02450
LS refinement shellResolution: 1.699→1.743 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 95 -
Rwork0.295 1986 -
all-2081 -
obs--81.67 %
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)
10.2775-0.1211-0.06810.1327-0.06260.4820.0077-0.0591-0.0073-0.0077-0.01130.0362-0.09580.08430.00360.11760.0078-0.00240.0606-0.01960.0237-28.11466.8175-30.1587
26.9325-4.04786.32013.6279-5.203913.40460.6415-0.77180.1712-0.13550.82550.0761-0.4008-0.8049-1.46710.1885-0.04220.21860.2178-0.0510.3709-9.97778.5676-10.0517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 217
2X-RAY DIFFRACTION2D27 - 43

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