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- PDB-4pl1: X-ray crystal structure of C118A RlmN from Escherichia coli with ... -

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Basic information

Entry
Database: PDB / ID: 4pl1
TitleX-ray crystal structure of C118A RlmN from Escherichia coli with S-adenosylmethionine
ComponentsDual-specificity RNA methyltransferase RlmN
KeywordsTRANSFERASE / RADICAL SAM / S-ADENOSYLMETHIONINE / IRON-SULFUR CLUSTER / METHYLTRANSFERASE / OXIDOREDUCTASE
Function / homology
Function and homology information


DNA polymerase; domain 1 - #530 / DNA polymerase; domain 1 / Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / :
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.58 Å
AuthorsBoal, A.K. / Rosenzweig, A.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN.
Authors: Silakov, A. / Grove, T.L. / Radle, M.I. / Bauerle, M.R. / Green, M.T. / Rosenzweig, A.C. / Boal, A.K. / Booker, S.J.
History
DepositionMay 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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
B: Dual-specificity RNA methyltransferase RlmN
A: Dual-specificity RNA methyltransferase RlmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4876
Polymers80,9872
Non-polymers1,5004
Water00
1
B: Dual-specificity RNA methyltransferase RlmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2443
Polymers40,4941
Non-polymers7502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Dual-specificity RNA methyltransferase RlmN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2443
Polymers40,4941
Non-polymers7502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.627, 55.729, 254.032
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: 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: 40493.539 Da / Num. of mol.: 2 / Fragment: UNP residues 17-375 / Mutation: C118A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1 / Gene: rlmN, EcDH1_1151, ECDH1ME8569_2444 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C9QPQ6, 23S rRNA (adenine2503-C2)-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 6000, HEPES, MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.58→30 Å / Num. obs: 24546 / % possible obs: 95.7 % / Redundancy: 5.9 % / Net I/σ(I): 16.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.58→28.85 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.858 / SU B: 15.628 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.633 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2998 1230 5.1 %RANDOM
Rwork0.2633 23121 --
obs0.2651 24351 94.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.85 Å2 / Biso mean: 57.534 Å2 / Biso min: 38.77 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å20 Å20 Å2
2---1.72 Å20 Å2
3----0.95 Å2
Refinement stepCycle: final / Resolution: 2.58→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5453 0 70 0 5523
Biso mean--58.02 --
Num. residues----691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.025627
X-RAY DIFFRACTIONr_bond_other_d0.0010.025478
X-RAY DIFFRACTIONr_angle_refined_deg1.0361.987621
X-RAY DIFFRACTIONr_angle_other_deg1.185312578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0025689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44523.946261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.105151013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2131550
X-RAY DIFFRACTIONr_chiral_restr0.0530.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021261
LS refinement shellResolution: 2.58→2.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 69 -
Rwork0.331 1429 -
all-1498 -
obs--78.64 %

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