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- PDB-3rf9: X-ray structure of RlmN from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 3rf9
TitleX-ray structure of RlmN from Escherichia coli
ComponentsRibosomal RNA large subunit methyltransferase N
KeywordsOXIDOREDUCTASE / radical sam / S-adenosylmethionine / iron sulfur cluster / methyltransferase
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 / cytosol
Similarity search - Function
Black beetle virus capsid protein - #60 / Black beetle virus capsid protein / : / 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. ...Black beetle virus capsid protein - #60 / Black beetle virus capsid protein / : / 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 / Few Secondary Structures / Irregular / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Dual-specificity RNA methyltransferase RlmN
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsBoal, A.K. / Grove, T.L. / McLaughlin, M.I. / Yennawar, N. / Booker, S.J. / Rosenzweig, A.C.
CitationJournal: Science / Year: 2011
Title: Structural basis for methyl transfer by a radical SAM enzyme.
Authors: Boal, A.K. / Grove, T.L. / McLaughlin, M.I. / Yennawar, N.H. / Booker, S.J. / Rosenzweig, A.C.
History
DepositionApr 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_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_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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal RNA large subunit methyltransferase N
B: Ribosomal RNA large subunit methyltransferase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4515
Polymers90,6302
Non-polymers8213
Water6,593366
1
B: Ribosomal RNA large subunit methyltransferase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7853
Polymers45,3151
Non-polymers4702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Ribosomal RNA large subunit methyltransferase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6662
Polymers45,3151
Non-polymers3521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.152, 80.406, 312.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-470-

HOH

21B-472-

HOH

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Components

#1: Protein Ribosomal RNA large subunit methyltransferase N / 23S rRNA m2A2503 methyltransferase


Mass: 45314.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rlmN, yfgB, b2517, JW2501 / Production host: Escherichia coli (E. coli)
References: UniProt: P36979, 23S rRNA (adenine2503-C2)-methyltransferase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 10% PEG 6000, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98, 1.65, 1.72
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
21.651
31.721
ReflectionResolution: 2.2→50 Å / Num. all: 46430 / Num. obs: 43897 / % possible obs: 99.3 % / Observed criterion σ(F): 47.7 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.086 / Χ2: 1.108 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.245.40.45320330.982192.3
2.24-2.2860.41921330.843196.4
2.28-2.326.50.39321300.838197.4
2.32-2.377.10.35321570.812199
2.37-2.427.40.30721510.811100
2.42-2.487.50.25721450.8441100
2.48-2.547.50.22621930.8451100
2.54-2.617.60.19721510.8461100
2.61-2.697.50.17521570.8951100
2.69-2.777.50.16321760.9691100
2.77-2.877.50.14121511.0411100
2.87-2.997.50.11821911.0681100
2.99-3.127.50.09821931.0721100
3.12-3.297.50.07921971.0871100
3.29-3.497.50.06221540.9411100
3.49-3.767.50.06422281.4741100
3.76-4.147.40.06421861.9721100
4.14-4.747.40.04722291.3911100
4.74-5.977.30.03922531.2181100
5.97-506.90.04923542.028199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 12.632 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 2333 5 %RANDOM
Rwork0.2133 ---
all0.2159 46430 --
obs0.2159 43562 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.92 Å2 / Biso mean: 35.4537 Å2 / Biso min: 10.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.53 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5593 0 24 366 5983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225714
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.977725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2555702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91123.829269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.929151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6281554
X-RAY DIFFRACTIONr_chiral_restr0.0710.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214254
X-RAY DIFFRACTIONr_mcbond_it0.391.53510
X-RAY DIFFRACTIONr_mcangle_it0.74925687
X-RAY DIFFRACTIONr_scbond_it1.02132204
X-RAY DIFFRACTIONr_scangle_it1.8014.52014
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 176 -
Rwork0.264 3050 -
all-3226 -
obs--93.1 %
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)
11.3533-0.2831.06410.4158-0.2170.94560.0669-0.0278-0.0519-0.0596-0.00250.01340.0859-0.035-0.06440.05750.0452-0.0470.0704-0.04670.044526.959910.367299.1421
20.2267-0.1384-0.07181.13650.90420.8986-0.0349-0.0250.0070.07480.1095-0.00730.06120.1762-0.07460.09380.0668-0.04040.0945-0.05970.0427-3.578312.2396135.5623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B14 - 374
2X-RAY DIFFRACTION2A10 - 374

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