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- PDB-5f8c: Rv2258c-unbound -

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Basic information

Entry
Database: PDB / ID: 5f8c
TitleRv2258c-unbound
ComponentsMethyltransferase
KeywordsTRANSFERASE / methyltransferase / Class I / sinefungin / S-adenosyl-L-homocysteine
Function / homology
Function and homology information


peptidoglycan-based cell wall / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / cellular response to hypoxia / methylation / 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
S-adenosylmethionine-dependent methyltransferase Rv2258c
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.83 Å
AuthorsIm, H.N. / Suh, S.W.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Korea Ministry of Science, ICT and Future Planning2013R1A2A1A05067303 Korea, Republic Of
Korea Ministry of Health, Welfare & Family AffairsA092006 Korea, Republic Of
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
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)121,8407
Polymers121,4723
Non-polymers3684
Water12,953719
1
A: Methyltransferase

A: Methyltransferase


Theoretical massNumber of molelcules
Total (without water)80,9812
Polymers80,9812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7440 Å2
ΔGint-66 kcal/mol
Surface area28680 Å2
MethodPISA
2
B: Methyltransferase
C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3506
Polymers80,9812
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-67 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.254, 140.635, 97.239
Angle α, β, γ (deg.)90.00, 98.56, 90.00
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 719 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.26 Å3/Da / Density % sol: 62.3 %
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: 0.92019 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92019 Å / Relative weight: 1
ReflectionResolution: 1.83→27.25 Å / Num. obs: 127941 / % possible obs: 99.9 % / Redundancy: 4.1 % / Net I/σ(I): 28.7
Reflection shellResolution: 1.83→1.86 Å / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data processing
PHENIXphasing
RefinementResolution: 1.83→27.25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.02 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22599 6387 5 %RANDOM
Rwork0.19077 ---
obs0.19252 120865 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-0 Å20.18 Å2
2---0.06 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.83→27.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8030 0 24 719 8773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198213
X-RAY DIFFRACTIONr_bond_other_d0.0020.027802
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.96611141
X-RAY DIFFRACTIONr_angle_other_deg0.923317885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64951072
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4123.683353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.895151299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0371559
X-RAY DIFFRACTIONr_chiral_restr0.0740.21284
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029450
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021847
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_it1.6583.1554291
X-RAY DIFFRACTIONr_mcbond_other1.6583.1544290
X-RAY DIFFRACTIONr_mcangle_it2.4694.725362
X-RAY DIFFRACTIONr_mcangle_other2.4684.725363
X-RAY DIFFRACTIONr_scbond_it2.3583.4583922
X-RAY DIFFRACTIONr_scbond_other2.3583.4583922
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7445.0735780
X-RAY DIFFRACTIONr_long_range_B_refined5.87725.9549750
X-RAY DIFFRACTIONr_long_range_B_other5.87625.9579751
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 482 -
Rwork0.286 8815 -
obs--98.78 %

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