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- PDB-5hr6: X-ray crystal structure of C118A RlmN with cross-linked tRNA puri... -

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Basic information

Entry
Database: PDB / ID: 5hr6
TitleX-ray crystal structure of C118A RlmN with cross-linked tRNA purified from Escherichia coli
Components
  • RlmN methylase
  • tRNA Glu
KeywordsTRANSFERASE/RNA / protein-RNA complex / radical SAM enzyme / transfer RNA / iron-sulfur cluster / TRANSFERASE-RNA complex
Function / homology
Function and homology information


23S rRNA (adenine2503-C2)-methyltransferase / tRNA (adenine(37)-C2)-methyltransferase activity / rRNA (adenine(2503)-C2-)-methyltransferase activity / tRNA methylation / rRNA base methylation / 4 iron, 4 sulfur cluster binding / tRNA binding / rRNA binding / response to antibiotic / metal ion binding ...23S rRNA (adenine2503-C2)-methyltransferase / tRNA (adenine(37)-C2)-methyltransferase activity / rRNA (adenine(2503)-C2-)-methyltransferase activity / tRNA methylation / rRNA base methylation / 4 iron, 4 sulfur cluster binding / tRNA binding / rRNA binding / response to antibiotic / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / Ribosomal RNA large subunit methyltransferase N-terminal domain / Ribosomal RNA large subunit methyltransferase RlmN/Cfr / Dual-specificity RNA methyltransferase RlmN / Methyltransferase (Class A) / DNA polymerase; domain 1 - #530 / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / DNA polymerase; domain 1 ...: / Ribosomal RNA large subunit methyltransferase N-terminal domain / Ribosomal RNA large subunit methyltransferase RlmN/Cfr / Dual-specificity RNA methyltransferase RlmN / Methyltransferase (Class A) / DNA polymerase; domain 1 - #530 / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / DNA polymerase; domain 1 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-DEOXYADENOSINE / METHIONINE / IRON/SULFUR CLUSTER / : / RNA / RNA (> 10) / Dual-specificity RNA methyltransferase RlmN / Dual-specificity RNA methyltransferase RlmN
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.88 Å
AuthorsSchwalm, E.L. / Grove, T.L. / Booker, S.J. / Boal, A.K.
CitationJournal: Science / Year: 2016
Title: Crystallographic capture of a radical S-adenosylmethionine enzyme in the act of modifying tRNA.
Authors: Schwalm, E.L. / Grove, T.L. / Booker, S.J. / Boal, A.K.
History
DepositionJan 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RlmN methylase
C: tRNA Glu
B: RlmN methylase
D: tRNA Glu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,86016
Polymers134,2104
Non-polymers1,65012
Water82946
1
A: RlmN methylase
C: tRNA Glu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9549
Polymers67,1052
Non-polymers8497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-72 kcal/mol
Surface area22810 Å2
MethodPISA
2
B: RlmN methylase
D: tRNA Glu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9057
Polymers67,1052
Non-polymers8015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-54 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.664, 69.821, 149.298
Angle α, β, γ (deg.)90.00, 90.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein RlmN methylase / 23S rRNA (adenine(2503)-C(2))-methyltransferase / 23S rRNA m2A2503 methyltransferase / Ribosomal ...23S rRNA (adenine(2503)-C(2))-methyltransferase / 23S rRNA m2A2503 methyltransferase / Ribosomal RNA large subunit methyltransferase N / tRNA (adenine(37)-C(2))-methyltransferase / tRNA m2A37 methyltransferase


Mass: 45296.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: A7ZPW0, UniProt: P36979*PLUS
#2: RNA chain tRNA Glu


Mass: 21807.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 937521852

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Non-polymers , 5 types, 58 molecules

#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.77 Å3/Da / Density % sol: 67.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, potassium chloride, magnesium chloride, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
21.03321
ReflectionResolution: 2.85→88.663 Å / Num. obs: 23364 / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.132 / Net I/av σ(I): 26.296 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
2.85-2.96.8199.6
2.9-2.956.8199.90.971
2.95-3.016.7199.50.822
3.01-3.076.811000.635
3.07-3.146.8199.50.575
3.14-3.216.811000.512
3.21-3.296.8199.60.446
3.29-3.386.8199.80.352
3.38-3.486.7199.50.298
3.48-3.596.6199.70.259
3.59-3.726.6199.90.232
3.72-3.876.4199.70.197
3.87-4.046.2199.30.163
4.04-4.266.1199.70.142
4.26-4.525.9199.20.123
4.52-4.875.8199.30.106
4.87-5.365.7199.70.099
5.36-6.145.711000.099
6.14-7.735.6199.80.09
7.73-88.6635.1199.20.066

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.88→88.663 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 24.292 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.659 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22811 1700 4.1 %RANDOM
Rwork0.18175 ---
obs0.18365 39727 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.823 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20.56 Å2
2--1.09 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.88→88.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 2845 76 46 8539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0168926
X-RAY DIFFRACTIONr_bond_other_d0.0020.026902
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.70812721
X-RAY DIFFRACTIONr_angle_other_deg1.178316008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8995706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69423.955268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.107151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0561552
X-RAY DIFFRACTIONr_chiral_restr0.0940.21418
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022030
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8245.3872836
X-RAY DIFFRACTIONr_mcbond_other3.8245.3862835
X-RAY DIFFRACTIONr_mcangle_it5.7388.0733538
X-RAY DIFFRACTIONr_mcangle_other5.7378.0753539
X-RAY DIFFRACTIONr_scbond_it4.9786.4756090
X-RAY DIFFRACTIONr_scbond_other4.9776.4746089
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1719.6439160
X-RAY DIFFRACTIONr_long_range_B_refined9.42954.83710795
X-RAY DIFFRACTIONr_long_range_B_other9.42854.84310786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.878→2.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 121 -
Rwork0.288 2724 -
obs--92.61 %
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)
10.3098-0.2124-0.22640.3765-0.1930.9080.05240.11130.07940.0263-0.0745-0.1040.022-0.15780.0220.1501-0.01670.02870.09860.02470.1133-3.6642-4.839555.6632
20.6415-0.2083-0.65560.2251-0.11161.38590.0840.29170.040.0234-0.1703-0.064-0.1098-0.14330.08630.15980.02120.0420.29280.05220.05638.2441-5.117423.9491
30.29890.2931-0.09460.4478-0.09440.9931-0.0301-0.0407-0.0240.02630.0068-0.14710.0118-0.14880.02330.13360.0395-0.02480.07450.00420.145340.7832-3.313318.8936
40.68380.40460.77180.36560.22411.33140.1348-0.183-0.0090.0354-0.1777-0.01640.1381-0.09050.0430.11520.037-0.03280.32010.04530.029152.7756-2.301350.318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 371
2X-RAY DIFFRACTION2C2 - 69
3X-RAY DIFFRACTION3B18 - 371
4X-RAY DIFFRACTION4D3 - 68

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