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- PDB-3p9n: Rv2966c of M. tuberculosis is a RsmD-like methyltransferase -

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Basic information

Entry
Database: PDB / ID: 3p9n
TitleRv2966c of M. tuberculosis is a RsmD-like methyltransferase
ComponentsPOSSIBLE METHYLTRANSFERASE (METHYLASE)
KeywordsTRANSFERASE / Rv2966c / AdoMet Binding / RNA methylase / RsmD / SAM-fold / RNA methyltransferase
Function / homology
Function and homology information


rRNA methylation / methyltransferase activity / nucleic acid binding
Similarity search - Function
Conserved hypothetical protein 95 / RNA methyltransferase, RsmD / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKumar, A. / Malhotra, K. / Saigal, K. / Sinha, K.M. / Taneja, B.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and functional characterization of Rv2966c protein reveals an RsmD-like methyltransferase from Mycobacterium tuberculosis and the role of its N-terminal domain in target recognition
Authors: Kumar, A. / Saigal, K. / Malhotra, K. / Sinha, K.M. / Taneja, B.
History
DepositionOct 18, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references

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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)20,0333
Polymers19,9151
Non-polymers1182
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)54.780, 54.780, 100.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein POSSIBLE METHYLTRANSFERASE (METHYLASE) / Putative uncharacterized protein


Mass: 19914.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT3044, Rv2966c / Plasmid: pET28-His10-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P95128, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100mM tris(7.4),3.0M potassium acetate, VAPOR DIFFUSION, HANGING 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 12, 2010
RadiationMonochromator: silicon mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→47.4 Å / Num. all: 14232 / Num. obs: 14223 / % possible obs: 99.94 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.949 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FHP
Resolution: 1.9→27.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.773 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22149 712 5 %RANDOM
Rwork0.17838 ---
obs0.18038 13511 99.94 %-
all-14232 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.019 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20.91 Å20 Å2
2--1.82 Å20 Å2
3----2.74 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1345 0 8 181 1534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221394
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9711902
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46920.52657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95615216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5791523
X-RAY DIFFRACTIONr_chiral_restr0.1020.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211065
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_it0.9351.5914
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63621455
X-RAY DIFFRACTIONr_scbond_it2.4133480
X-RAY DIFFRACTIONr_scangle_it3.8174.5443
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 51 -
Rwork0.182 955 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -29.1623 Å / Origin y: 14.9662 Å / Origin z: 7.4965 Å
111213212223313233
T0.0785 Å20.001 Å2-0.0022 Å2-0.0122 Å20.0061 Å2--0.0465 Å2
L0.8418 °2-0.2686 °2-0.2521 °2-0.5099 °20.3194 °2--1.8907 °2
S-0.0784 Å °-0.0678 Å °0.0466 Å °0.0538 Å °0.0473 Å °-0.0037 Å °0.151 Å °0.091 Å °0.0311 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 19
2X-RAY DIFFRACTION1A26 - 184

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