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- PDB-7cfe: Crystal structure of RsmG methyltransferase of M. tuberculosis -

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Basic information

Entry
Database: PDB / ID: 7cfe
TitleCrystal structure of RsmG methyltransferase of M. tuberculosis
ComponentsRibosomal RNA small subunit methyltransferase G
KeywordsTRANSFERASE / Rossmann fold / RsmG / Rv3919c / M. tuberculosis / gidB
Function / homology
Function and homology information


rRNA (guanine-N7-)-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / plasma membrane / cytosol
Similarity search - Function
rRNA small subunit methyltransferase G / rRNA small subunit methyltransferase G / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / PHOSPHATE ION / SINEFUNGIN / Ribosomal RNA small subunit methyltransferase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.02 Å
AuthorsBijpuria, S. / Maurya, A. / Kumar, P. / Sharma, R. / Taneja, B.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EMR/2016/003589 India
CitationJournal: To Be Published
Title: Crystal structure of RsmG methyltransferase of M. tuberculosis
Authors: Bijpuria, S. / Maurya, A. / Kumar, P. / Sharma, R. / Taneja, B.
History
DepositionJun 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal RNA small subunit methyltransferase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4324
Polymers24,8961
Non-polymers5363
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-4 kcal/mol
Surface area9990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.980, 63.880, 72.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosomal RNA small subunit methyltransferase G / / 16S rRNA 7-methylguanosine methyltransferase / 16S rRNA m7G methyltransferase / Glucose-inhibited ...16S rRNA 7-methylguanosine methyltransferase / 16S rRNA m7G methyltransferase / Glucose-inhibited division protein B


Mass: 24895.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: rsmG, gidB, Rv3919c, MTV028.10c / Production host: Mycolicibacterium smegmatis (bacteria)
References: UniProt: P9WGW9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.06 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 296 K / Method: vapor diffusion
Details: 0.1 M Bis-tris pH 7.5, 0.18 M Na/K phosphate and 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.02→27.26 Å / Num. obs: 13090 / % possible obs: 98.7 % / Redundancy: 5.6 % / CC1/2: 0.991 / Net I/σ(I): 6.6
Reflection shellResolution: 2.02→2.07 Å / Num. unique obs: 799 / CC1/2: 0.532

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
iMOSFLMdata reduction
iMOSFLMdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.02→27.26 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 609 4.67 %
Rwork0.1881 --
obs0.1899 13047 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→27.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1616 0 36 154 1806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081693
X-RAY DIFFRACTIONf_angle_d0.972299
X-RAY DIFFRACTIONf_dihedral_angle_d19.43636
X-RAY DIFFRACTIONf_chiral_restr0.06264
X-RAY DIFFRACTIONf_plane_restr0.007299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.220.27481470.22412914X-RAY DIFFRACTION95
2.22-2.540.25511570.19843104X-RAY DIFFRACTION100
2.54-3.210.2171400.19983157X-RAY DIFFRACTION100
3.21-27.260.20671650.16823263X-RAY DIFFRACTION100

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