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- PDB-5hr7: X-ray crystal structure of C118A RlmN from Escherichia coli with ... -

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Basic information

Entry
Database: PDB / ID: 5hr7
TitleX-ray crystal structure of C118A RlmN from Escherichia coli with cross-linked in vitro transcribed tRNA
Components
  • Dual-specificity RNA methyltransferase RlmN
  • tRNA Glu
KeywordsOXIDOREDUCTASE/RNA / protein-RNA complex / radical SAM enzyme / transfer RNA / iron-sulfur cluster / OXIDOREDUCTASE-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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: tRNA Glu
C: tRNA Glu
B: Dual-specificity RNA methyltransferase RlmN
A: Dual-specificity RNA methyltransferase RlmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,23317
Polymers139,5594
Non-polymers1,67413
Water1,69394
1
D: tRNA Glu
A: Dual-specificity RNA methyltransferase RlmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6048
Polymers69,7792
Non-polymers8256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-68 kcal/mol
Surface area24230 Å2
MethodPISA
2
C: tRNA Glu
B: Dual-specificity RNA methyltransferase RlmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6299
Polymers69,7792
Non-polymers8497
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-70 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.717, 70.383, 151.810
Angle α, β, γ (deg.)90.000, 90.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain / Protein , 2 types, 4 molecules DCBA

#1: RNA chain tRNA Glu


Mass: 24378.514 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: RNA was prepared by in vitro transcription with T7 RNA polymerase
Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 944398239
#2: Protein Dual-specificity RNA methyltransferase RlmN / 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: 45400.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rlmN, EcE24377A_2801 / Production host: Escherichia coli (E. coli)
References: UniProt: A7ZPW0, UniProt: P36979*PLUS, 23S rRNA (adenine2503-C2)-methyltransferase

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Non-polymers , 5 types, 107 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#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-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: PEG 4000, sodium chloride, sodium cacodylate trihydrate, spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 75380 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.8 / Rmerge(I) obs: 0.087 / Net I/σ(I): 34.9
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 1.8 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RFA,2DER

3rfa

2der


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.669 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.212
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 3788 5 %RANDOM
Rwork0.2158 ---
obs0.2174 71560 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 141.32 Å2 / Biso mean: 62.237 Å2 / Biso min: 35.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5678 2972 77 94 8821
Biso mean--54.09 55.05 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0169186
X-RAY DIFFRACTIONr_bond_other_d0.0010.027100
X-RAY DIFFRACTIONr_angle_refined_deg1.011.70513104
X-RAY DIFFRACTIONr_angle_other_deg1.612316470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60623.942274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.189151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4671554
X-RAY DIFFRACTIONr_chiral_restr0.0750.21456
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022094
X-RAY DIFFRACTIONr_mcbond_it1.9885.8622894
X-RAY DIFFRACTIONr_mcbond_other1.9885.862893
X-RAY DIFFRACTIONr_mcangle_it3.2998.7853614
LS refinement shellResolution: 2.397→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 284 -
Rwork0.331 5135 -
all-5419 -
obs--97.22 %

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