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- PDB-3v8v: Crystal structure of bifunctional methyltransferase YcbY (RlmLK) ... -

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Basic information

Entry
Database: PDB / ID: 3v8v
TitleCrystal structure of bifunctional methyltransferase YcbY (RlmLK) from Escherichia coli, SAM binding
ComponentsRibosomal RNA large subunit methyltransferase L
KeywordsTRANSFERASE / YcbY / RNA methyltransferase / ribosome RNA / SAH / RlmKL / RlmL
Function / homology
Function and homology information


23S rRNA (guanine2445-N2)-methyltransferase / 23S rRNA (guanine2069-N7)-methyltransferase / 23S rRNA (guanine(2445)-N(2))-methyltransferase activity / rRNA (guanine-N2-)-methyltransferase activity / rRNA (guanine-N7-)-methyltransferase activity / rRNA base methylation / rRNA methylation / RNA binding / cytoplasm
Similarity search - Function
Ribosomal RNA large subunit methyltransferase K/L / : / RlmL ferredoxin-like domain / : / Uncharacterized protein family UPF0020 signature. / RNA methyltransferase domain (HRMD) like / S-adenosylmethionine-dependent methyltransferase / S-adenosylmethionine-dependent methyltransferase / VC0802-like - #30 / Ribosomal RNA large subunit methyltransferase K/L-like, FLD domain ...Ribosomal RNA large subunit methyltransferase K/L / : / RlmL ferredoxin-like domain / : / Uncharacterized protein family UPF0020 signature. / RNA methyltransferase domain (HRMD) like / S-adenosylmethionine-dependent methyltransferase / S-adenosylmethionine-dependent methyltransferase / VC0802-like - #30 / Ribosomal RNA large subunit methyltransferase K/L-like, FLD domain / RMKL-like, methyltransferase domain / THUMP / THUMP domain / THUMP domain / THUMP domain profile. / VC0802-like / Transcription Regulator spoIIAA / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
octanoyl-sucrose, esterificated at fructose C6 / S-ADENOSYLMETHIONINE / Ribosomal RNA large subunit methyltransferase K/L
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSu, X.D. / Wang, K.T.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA
Authors: Wang, K.T. / Desmolaize, B. / Nan, J. / Zhang, X.W. / Li, L.F. / Douthwaite, S. / Su, X.D.
History
DepositionDec 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 L
B: Ribosomal RNA large subunit methyltransferase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,4538
Polymers157,9222
Non-polymers2,5316
Water6,702372
1
A: Ribosomal RNA large subunit methyltransferase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2264
Polymers78,9611
Non-polymers1,2653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribosomal RNA large subunit methyltransferase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2264
Polymers78,9611
Non-polymers1,2653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.724, 140.586, 102.097
Angle α, β, γ (deg.)90.00, 101.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosomal RNA large subunit methyltransferase L / rlmLK / 23S rRNA m2G2445 methyltransferase / rRNA (guanine-N(2)-)-methyltransferase RlmL


Mass: 78961.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rlmL / Production host: Escherichia coli (E. coli)
References: UniProt: P75864, 23S rRNA (guanine2445-N2)-methyltransferase
#2: Polysaccharide 6-O-octanoyl-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / octanoyl-sucrose / esterificated at fructose C6


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 468.493 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: octanoyl-sucrose, esterificated at fructose C6
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_6*OCCCCCCCC/3=O][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES, 12%(w/v) PEG 8000 , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 62236 / Num. obs: 58938 / % possible obs: 94.7 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 4.8
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.6-2.69176.5
2.69-2.8186.3
2.8-2.93194.9
2.93-3.08199.3
3.08-3.28199.9
3.28-3.531100
3.53-3.88190.3
3.88-4.451100
4.45-5.61100
5.6-50199.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B78, 3LDG, 3LDF

2b78

3ldg

3ldf


Resolution: 2.6→42.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.907 / SU B: 21.515 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24694 3015 5.1 %RANDOM
Rwork0.18212 ---
obs0.18544 55890 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.339 Å2
Baniso -1Baniso -2Baniso -3
1-3.38 Å20 Å2-4.33 Å2
2---3.96 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9911 0 157 372 10440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02110299
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.9713987
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61451287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3423.685445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.927151611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0811571
X-RAY DIFFRACTIONr_chiral_restr0.140.21567
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217746
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.891.56453
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7210205
X-RAY DIFFRACTIONr_scbond_it2.65133846
X-RAY DIFFRACTIONr_scangle_it4.3594.53780
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.604→2.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 187 -
Rwork0.219 3209 -
obs--74.52 %
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)
11.93080.01910.74330.27430.16561.22520.0535-0.08480.0161-0.0037-0.0823-0.01420.0608-0.18480.02880.16220.0149-0.02070.08860.00050.068-9.1732.05612.848
20.5992-0.2690.8060.3518-0.77024.0839-0.11970.01840.13670.1071-0.04480.0023-0.30910.06330.16450.3823-0.0622-0.09330.01690.00430.070428.1680.44459.931
30.2529-0.4934-0.13161.6937-0.31534.86890.1417-0.0047-0.1194-0.3495-0.04470.49020.4043-0.3563-0.0970.4553-0.0621-0.20450.0423-0.01120.198514.13-33.84155.421
41.1039-0.35011.12522.11340.47351.65320.1495-0.0022-0.16220.26330.0144-0.01990.2398-0.0125-0.16390.2440.0323-0.08670.0647-0.01250.0843-3.404-32.586-2.56
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 390
2X-RAY DIFFRACTION2A391 - 702
3X-RAY DIFFRACTION3B1 - 382
4X-RAY DIFFRACTION4B393 - 702

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