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Basic information

Entry
Database: PDB / ID: 5f8f
TitleRv2258c-SFG
ComponentsMethyltransferase
KeywordsTRANSFERASE / methyltransferase / Class I / sinefungin / S-adenosyl-L-homocysteine / complex
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / peptidoglycan-based cell wall / methyltransferase activity / methylation / cellular response to hypoxia / plasma membrane
Similarity search - Function
: / Rv2258c-like winged HTH domain / Methyltransferase domain / Methyltransferase domain / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / S-adenosylmethionine-dependent methyltransferase Rv2258c
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsIm, H.N. / Suh, S.W.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S-adenosyl-l-methionine-dependent methyltransferase
Authors: Im, H.N. / Kim, H.S. / An, D.R. / Jang, J.Y. / Kim, J. / Yoon, H.J. / Yang, J.K. / Suh, S.W.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8929
Polymers121,4723
Non-polymers1,4206
Water12,556697
1
A: Methyltransferase
B: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0207
Polymers80,9812
Non-polymers1,0395
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-67 kcal/mol
Surface area28170 Å2
MethodPISA
2
C: Methyltransferase
hetero molecules

C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7444
Polymers80,9812
Non-polymers7632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area7360 Å2
ΔGint-65 kcal/mol
Surface area27930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.958, 141.118, 96.970
Angle α, β, γ (deg.)90.000, 98.380, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyltransferase / / Possible transcriptional regulatory protein


Mass: 40490.605 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv2258c, LH57_12310 / Production host: Escherichia coli (E. coli) / References: UniProt: O53532
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 3.31 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: sodium malonate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 113690 / % possible obs: 99.9 % / Redundancy: 4 % / Net I/σ(I): 28.8
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementResolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.93 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 5682 5 %RANDOM
Rwork0.1925 ---
obs0.194 107815 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.4 Å2 / Biso mean: 37.958 Å2 / Biso min: 20.06 Å2
Baniso -1Baniso -2Baniso -3
1-4.05 Å2-0 Å21.2 Å2
2---1.42 Å2-0 Å2
3----2.86 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8000 0 99 697 8796
Biso mean--44.18 44.08 -
Num. residues----1068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198241
X-RAY DIFFRACTIONr_bond_other_d0.0030.027816
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.97911187
X-RAY DIFFRACTIONr_angle_other_deg1.0033.00517922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67951065
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39323.754349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.171151290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2671558
X-RAY DIFFRACTIONr_chiral_restr0.0810.21296
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021836
X-RAY DIFFRACTIONr_mcbond_it2.033.6094278
X-RAY DIFFRACTIONr_mcbond_other2.033.6094278
X-RAY DIFFRACTIONr_mcangle_it2.9235.3985337
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 427 -
Rwork0.276 7952 -
all-8379 -
obs--99.93 %

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