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- PDB-7f8b: Crystal structure of rRNA methyltransferase Erm38 in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 7f8b
TitleCrystal structure of rRNA methyltransferase Erm38 in complex with SAM
ComponentsErm(38)
KeywordsTRANSFERASE / erythromycin resistance methyltransferase / methyltransferase / SAM
Function / homology
Function and homology information


rRNA (adenine-N6,N6-)-dimethyltransferase activity / RNA binding
Similarity search - Function
Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / SUCCINIC ACID / Erm(38)
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 Å
AuthorsGoh, B.C. / Lescar, J.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structure and functional analysis of mycobacterial erythromycin resistance methyltransferase Erm38 reveals its RNA-binding site.
Authors: Goh, B.C. / Xiang, X. / Lescar, J. / Dedon, P.C.
History
DepositionJul 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Erm(38)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5584
Polymers28,9231
Non-polymers6353
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint3 kcal/mol
Surface area12530 Å2
Unit cell
Length a, b, c (Å)78.018, 78.018, 101.536
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Erm(38)


Mass: 28923.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: erm(38) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q79N53
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.0 M succinic acid pH 7, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.248→48.47 Å / Num. obs: 15503 / % possible obs: 99.8 % / Redundancy: 25.9 % / Biso Wilson estimate: 48.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.016 / Rrim(I) all: 0.08 / Net I/σ(I): 31.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.25-2.3223.30.83134313440.9370.1670.8184.497.5
8.99-48.47210.023647830810.0050.02495.399.6

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F8A

7f8a


Resolution: 2.248→48.47 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.283 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 761 4.92 %RANDOM
Rwork0.211 ---
obs0.2129 15465 99.7 %-
Displacement parametersBiso max: 89.73 Å2 / Biso mean: 43.78 Å2 / Biso min: 23.29 Å2
Baniso -1Baniso -2Baniso -3
1-4.4054 Å20 Å20 Å2
2--4.4054 Å20 Å2
3----8.8109 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.248→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 43 151 2085
Biso mean--63.75 51.97 -
Num. residues----245
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d661SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes330HARMONIC5
X-RAY DIFFRACTIONt_it1980HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion263SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1669SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1980HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2703HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion12.91
LS refinement shellResolution: 2.25→2.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 39
RfactorNum. reflection% reflection
Rfree0.3535 17 4.18 %
Rwork0.2236 390 -
all0.2283 407 -
obs--89.89 %

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