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- PDB-4poo: The crystal structure of Bacillus subtilis YtqB in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 4poo
TitleThe crystal structure of Bacillus subtilis YtqB in complex with SAM
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
S-ADENOSYLMETHIONINE / Putative RNA methylase
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3774
Polymers43,5802
Non-polymers7972
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-11 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.066, 77.661, 100.481
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
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A6 - 11
2115B6 - 11
1215A13 - 21
2215B13 - 21
1315A24 - 53
2315B24 - 53
1415A56 - 151
2415B56 - 151
1515A154 - 158
2515B154 - 158
1615A161 - 166
2615B161 - 166
1715A168 - 176
2715B168 - 176
1815A180 - 188
2815B180 - 188
1121A301
2121B301

NCS ensembles :
ID
1
2

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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: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30-36% PEG200/5% PEG2000/0.1M sodium cacodylate (pH 6.5) or 30-36% PEG200/5% PEG2000/0.1 M Hepes (pH 7.0) , VAPOR DIFFUSION, SITTING DROP, temperature 291 K
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)
DetectorType: ADSC QUANTUM 270 / Detector: CCD
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 19185 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.28 Å / % possible all: 98.4

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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: 4PON

4pon


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.6 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25995 982 5.1 %RANDOM
Rwork0.22013 ---
obs0.22207 18155 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.166 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--0.41 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 54 10 2659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222695
X-RAY DIFFRACTIONr_bond_other_d0.0010.021719
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9833659
X-RAY DIFFRACTIONr_angle_other_deg0.97734232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5265342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9725.185108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69915423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.417158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022983
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
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_it0.7011.51730
X-RAY DIFFRACTIONr_mcbond_other0.1981.5715
X-RAY DIFFRACTIONr_mcangle_it1.23922749
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2153965
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5044.5910
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
22B41tight positional0.070.05
11A865medium positional0.180.5
11A910loose positional0.415
22B41tight thermal0.230.5
11A865medium thermal0.672
11A910loose thermal0.8510
LS refinement shellResolution: 2.2→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 73 -
Rwork0.245 1271 -
obs--95.45 %
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)
14.4222.68420.64345.80321.83095.89760.2122-0.1663-0.01580.1054-0.2647-0.3125-0.52420.32090.05250.6474-0.07880.00780.1285-0.03520.214613.830.071117.907
22.28210.2471-0.31255.64191.11763.12510.1456-0.19130.24380.1644-0.31060.6728-0.0644-0.31740.1650.5510.0026-0.00120.227-0.12770.27181.18920.286115.367
32.0407-0.23940.20217.03050.9972.3778-0.0080.0924-0.2278-0.8008-0.0158-0.5727-0.06320.09890.02370.46630.00290.10130.0498-0.00820.20619.815-7.39997.096
41.25550.9766-0.468710.99891.28721.85820.1394-0.3728-0.11740.5267-0.34090.350.0144-0.23580.20140.5276-0.0430.01580.2229-0.0230.15743.487-1.797111.186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 109
2X-RAY DIFFRACTION2A112 - 190
3X-RAY DIFFRACTION3B0 - 102
4X-RAY DIFFRACTION4B116 - 190

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