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- PDB-4l69: Rv2372c of Mycobacterium tuberculosis is RsmE like methyltransferse -

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Basic information

Entry
Database: PDB / ID: 4l69
TitleRv2372c of Mycobacterium tuberculosis is RsmE like methyltransferse
ComponentsRibosomal RNA small subunit methyltransferase E
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


rRNA (uridine-N3-)-methyltransferase activity / 16S rRNA (uracil1498-N3)-methyltransferase / rRNA base methylation / methyltransferase activity / rRNA processing / methylation / cytoplasm
Similarity search - Function
Hypothetical PUA domain-like; domain 1 / Ribosomal RNA small subunit methyltransferase E / RNA methyltransferase domain / Ribosomal Protein L25; Chain P / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / PUA-like superfamily / Beta Barrel ...Hypothetical PUA domain-like; domain 1 / Ribosomal RNA small subunit methyltransferase E / RNA methyltransferase domain / Ribosomal Protein L25; Chain P / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / PUA-like superfamily / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase E / Ribosomal RNA small subunit methyltransferase E
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKumar, A. / Taneja, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The structure of Rv2372c identifies an RsmE-like methyltransferase from Mycobacterium tuberculosis
Authors: Kumar, A. / Kumar, S. / Taneja, B.
History
DepositionJun 12, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal RNA small subunit methyltransferase E


Theoretical massNumber of molelcules
Total (without water)27,7741
Polymers27,7741
Non-polymers00
Water34219
1
A: Ribosomal RNA small subunit methyltransferase E

A: Ribosomal RNA small subunit methyltransferase E


Theoretical massNumber of molelcules
Total (without water)55,5482
Polymers55,5482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2570 Å2
ΔGint-19 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.940, 81.940, 115.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ribosomal RNA small subunit methyltransferase E / / 16S rRNA m3U1498 methyltransferase


Mass: 27773.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT2441, MTCY27.08, rsmE, Rv2372c / Plasmid: pET28-His10-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: P67202, UniProt: P9WGX1*PLUS, 16S rRNA (uracil1498-N3)-methyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.48 Å3/Da / Density % sol: 64.63 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9762 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 18, 2012 / Details: mirrors
RadiationMonochromator: silicon mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.9→57.94 Å / Num. all: 8852 / Num. obs: 8836 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Biso Wilson estimate: 93.67 Å2 / Rmerge(I) obs: 0.067
Reflection shellHighest resolution: 2.9 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VHY
Resolution: 2.9→51.75 Å / Cor.coef. Fo:Fc: 0.9255 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.43 / SU R Cruickshank DPI: 0.591 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.655 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.31
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 416 4.72 %RANDOM
Rwork0.1993 ---
obs0.2009 8822 96 %-
Displacement parametersBiso max: 228.51 Å2 / Biso mean: 96.24 Å2 / Biso min: 50.67 Å2
Baniso -1Baniso -2Baniso -3
1--15.1127 Å20 Å20 Å2
2---15.1127 Å20 Å2
3---30.2255 Å2
Refine analyzeLuzzati coordinate error obs: 0.495 Å
Refinement stepCycle: LAST / Resolution: 2.9→51.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 0 19 1771
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d585SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes274HARMONIC5
X-RAY DIFFRACTIONt_it1778HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion240SEMIHARMONIC5
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_contact2003SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1778HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2433HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion2.15
X-RAY DIFFRACTIONt_other_torsion19.92
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3202 124 5.02 %
Rwork0.2277 2348 -
all0.2325 2472 -
obs--96 %
Refinement TLS params.Method: refined / Origin x: -9.3736 Å / Origin y: 27.4704 Å / Origin z: 27.0956 Å
111213212223313233
T-0.1905 Å20.1242 Å20.0438 Å2--0.2416 Å2-0.0506 Å2---0.1546 Å2
L2.4187 °20.3221 °20.1275 °2-2.4743 °2-1.1938 °2--4.5348 °2
S0.1031 Å °-0.1531 Å °0.0206 Å °-0.049 Å °-0.1326 Å °-0.0258 Å °-0.1226 Å °0.1837 Å °0.0295 Å °
Refinement TLS groupSelection details: { A|* }

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