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- PDB-6m1c: Crystal structure of RsmD methyltransferase of M. tuberculosis in... -

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Basic information

Entry
Database: PDB / ID: 6m1c
TitleCrystal structure of RsmD methyltransferase of M. tuberculosis in complex with sinefungin reveals key interactions
ComponentsPossible methyltransferase (Methylase)
KeywordsTRANSFERASE / Rossmann fold / RsmD / Rv2966c / M. tuberculosis
Function / homology
Function and homology information


rRNA methylation / methyltransferase activity / nucleic acid binding
Similarity search - Function
RNA methyltransferase, RsmD / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase
Similarity search - Domain/homology
ACETATE ION / SINEFUNGIN / Possible methyltransferase (Methylase)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsBijpuria, S. / Khan, S.H. / Kumar, A. / 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 RsmD methyltransferase of M. tuberculosis in complex with sinefungin reveals key interactions
Authors: Bijpuria, S. / Khan, S.H. / Kumar, A. / Taneja, B.
History
DepositionFeb 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Possible methyltransferase (Methylase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3553
Polymers19,9151
Non-polymers4402
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)55.191, 55.191, 99.641
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

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Components

#1: Protein Possible methyltransferase (Methylase)


Mass: 19914.572 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: Rv2966c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I6XFS7
#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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.21 Å3/Da / Density % sol: 44.47 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.1 MTris-HCl, 3.2 M Potassium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.887821 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.887821 Å / Relative weight: 1
ReflectionResolution: 2.4→47.8 Å / Num. obs: 7293 / % possible obs: 100 % / Redundancy: 9.2 % / CC1/2: 0.999 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 745 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P9N
Resolution: 2.401→47.8 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.73
RfactorNum. reflection% reflection
Rfree0.2361 404 5.58 %
Rwork0.2034 --
obs0.2052 7238 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.401→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1363 0 31 53 1447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071434
X-RAY DIFFRACTIONf_angle_d0.8381960
X-RAY DIFFRACTIONf_dihedral_angle_d16.877847
X-RAY DIFFRACTIONf_chiral_restr0.049235
X-RAY DIFFRACTIONf_plane_restr0.006253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.401-2.74840.32641460.2452204X-RAY DIFFRACTION99
2.7484-3.46260.29331370.22332253X-RAY DIFFRACTION100
3.4626-47.80.18991210.18632377X-RAY DIFFRACTION100

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