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- PDB-4pon: The crystal structure of a putative SAM-dependent methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 4pon
TitleThe crystal structure of a putative SAM-dependent methyltransferase, YtqB, from Bacillus subtilis
ComponentsPutative RNA methylase
KeywordsTRANSFERASE / Rossmann-like fold / a putative methyltransferase / S-adenosyl-L-methionine
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
Putative rRNA methylase / Putative rRNA methylase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative RNA methylase
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPark, S.C. / Song, W.S. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Structural analysis of a putative SAM-dependent methyltransferase, YtqB, from Bacillus subtilis
Authors: Park, S.C. / Song, W.S. / Yoon, S.I.
History
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative RNA methylase
B: Putative RNA methylase


Theoretical massNumber of molelcules
Total (without water)43,5802
Polymers43,5802
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-13 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.859, 76.570, 100.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 6 / Auth seq-ID: 1 - 191 / Label seq-ID: 7 - 197

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Putative RNA methylase


Mass: 21789.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. spizizenii (bacteria)
Strain: ATCC 23059 / NRRL B-14472 / W23 / Gene: BSUW23_14785, ytqB / Plasmid: a modified pET49b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E0TY72
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30-36% PEG200/5% PEG2000/0.1 M sodium cacodylate (pH 6.5) or 30-36% PEG200/5% PEG2000/0.1 M Hepes (pH 7.0), VAPOR DIFFUSION, SITTING DROP, temperature 291K
PH range: 6.5, 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97958 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 24, 2013
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 30744 / Num. obs: 30744 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EEY

3eey


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.813 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23595 1526 5 %RANDOM
Rwork0.20005 ---
obs0.20192 28698 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.809 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2629 0 0 154 2783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222688
X-RAY DIFFRACTIONr_bond_other_d0.0010.021778
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9633631
X-RAY DIFFRACTIONr_angle_other_deg0.94734387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83225.75120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21515478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.84158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02494
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_it0.8611.51703
X-RAY DIFFRACTIONr_mcbond_other0.2311.5702
X-RAY DIFFRACTIONr_mcangle_it1.51822723
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3523985
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.864.5905
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2137 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.385
Bloose thermal2.0110
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 95 -
Rwork0.241 2094 -
obs--99.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8629-1.6691-0.02475.72190.95121.68930.13090.12410.0317-0.2951-0.13430.03220.06120.09380.00340.24410.0337-0.01290.0624-0.00330.1567-10.779-29.554-16.279
21.96-1.5661-0.50310.42221.22731.04980.02660.0769-0.3841-0.2042-0.31311.49770.0801-0.11460.28640.202-0.0125-0.01710.0443-0.08760.3819-23.925-20.543-12.584
31.31670.68-0.1883.10430.30341.2412-0.0705-0.15680.08520.33190.093-0.26680.06090.0463-0.02250.15830.0197-0.05570.0316-0.03830.2138-16.6797.6983.784
41.6565-0.0711-0.28825.39350.73081.7874-0.07340.17940.0102-0.31520.01810.0004-0.0287-0.04620.05530.1422-0.0152-0.01350.0233-0.01690.1281-21.4461.68-10.727
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION2A115 - 191
3X-RAY DIFFRACTION3B1 - 103
4X-RAY DIFFRACTION4B116 - 191

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