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- PDB-3gyq: Structure of the Thiostrepton-Resistance Methyltransferase S-aden... -

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Basic information

Entry
Database: PDB / ID: 3gyq
TitleStructure of the Thiostrepton-Resistance Methyltransferase S-adenosyl-L-methionine Complex
ComponentsrRNA (adenosine-2'-O-)-methyltransferase23S rRNA (adenosine1067-2'-O)-methyltransferase
KeywordsTRANSFERASE / rRNA Methyltransferase / SPOUT MTases / SAM / Trefoil knot / Antibiotic resistance / Methyltransferase / S-adenosyl-L-methionine
Function / homology
Function and homology information


23S rRNA (adenosine1067-2'-O)-methyltransferase / 23S rRNA (adenosine(1067)-2'-O)-methyltransferase activity / response to antibiotic / RNA binding
Similarity search - Function
Thiostrepton-resistance methylase, N-terminal / Thiostrepton-resistance methylase, N terminus / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / Ribosomal protein L30/S12 / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 60s Ribosomal Protein L30; Chain: A; ...Thiostrepton-resistance methylase, N-terminal / Thiostrepton-resistance methylase, N terminus / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / Ribosomal protein L30/S12 / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 60s Ribosomal Protein L30; Chain: A; / 50S ribosomal protein L30e-like / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / 23S rRNA (adenosine(1067)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesStreptomyces cyaneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDunstan, M.S. / Conn, G.L.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure of the thiostrepton-resistance methyltransferase-S-adenosyl-L-methionine complex and its interaction with ribosomal RNA
Authors: Dunstan, M.S. / Hang, P.C. / Zelinskaya, N.V. / Honek, J.F. / Conn, G.L.
History
DepositionApr 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: rRNA (adenosine-2'-O-)-methyltransferase
B: rRNA (adenosine-2'-O-)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2274
Polymers58,4312
Non-polymers7972
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-10 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.960, 55.770, 215.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein rRNA (adenosine-2'-O-)-methyltransferase / 23S rRNA (adenosine1067-2'-O)-methyltransferase / Thiostrepton Resistance methyltransferase / 23S rRNA [AM1067] 2'-O-methyltransferase / 23S rRNA ...Thiostrepton Resistance methyltransferase / 23S rRNA [AM1067] 2'-O-methyltransferase / 23S rRNA methylase / Thiostrepton-resistance methylase


Mass: 29215.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cyaneus (bacteria) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLysS / References: UniProt: P18644, EC: 2.1.1.66
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


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


Mass: 18.015 Da / Num. of mol.: 72 / 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: 293 K / Method: vapor diffusion / pH: 8
Details: 27% PEG 4000, 0.2M sodium acetate, 0.1M Tris buffer pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.45→19.6 Å / Num. obs: 18976 / % possible obs: 95.8 % / Observed criterion σ(F): 2.45 / Observed criterion σ(I): 2.85 / Redundancy: 4.4 % / Biso Wilson estimate: 60.5 Å2 / Rsym value: 0.107 / Net I/σ(I): 10.2
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.85 / Rsym value: 0.365 / % possible all: 90

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
DNAdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ipa

1ipa


Resolution: 2.45→19.388 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.814 / SU ML: 0.17 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.268 989 5.23 %RANDOM
Rwork0.215 ---
all0.2179 18974 --
obs0.218 18914 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.213 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 256.17 Å2 / Biso mean: 79.618 Å2 / Biso min: 19.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.235 Å2-0 Å2-0 Å2
2--0.262 Å20 Å2
3----1.427 Å2
Refinement stepCycle: LAST / Resolution: 2.45→19.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3922 0 54 72 4048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024032
X-RAY DIFFRACTIONf_angle_d0.635460
X-RAY DIFFRACTIONf_chiral_restr0.042648
X-RAY DIFFRACTIONf_plane_restr0.003714
X-RAY DIFFRACTIONf_dihedral_angle_d15.7361532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.5790.3071290.23725372666100
2.579-2.740.2981300.23525242654100
2.74-2.9510.2781450.23625072652100
2.951-3.2470.3191330.22125382671100
3.247-3.7140.241470.21425702717100
3.714-4.6680.2371520.18925682720100
4.668-19.3880.2641530.22681283499
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)
10.56630.05860.62440.386-1.03431.0286-0.06170.3013-0.42760.659-0.3454-0.02351.11440.4599-0.00531.77390.04210.07030.7616-0.20750.790428.1896-0.034564.4283
21.7652-0.9854-1.20673.55530.99384.9980.13110.53210.2061-0.79630.28990.0955-0.2156-0.38610.00040.4834-0.0765-0.07610.50970.18760.21789.858923.455971.1636
33.41351.65651.30482.2941-0.72953.8353-0.0055-0.0397-0.1462-0.30870.022-0.10330.2001-0.08450.00020.19980.02840.04080.23750.10320.332217.891915.13394.6801
41.78180.1657-0.75712.6878-0.35591.13280.2235-0.14640.37290.0804-0.07820.025-0.73910.16730.00030.5258-0.04890.03720.38410.02910.47230.05142.832693.4814
5-0.00160.0612-0.0064-0.01170.0194-0.3188-0.27060.42850.2380.03870.1747-0.2901-0.5541.29840.00070.65360.00040.30960.7786-0.11350.938713.333529.95280.7479
6-0.7920.0226-0.1021-0.19520.12520.74860.33450.54080.2353-0.76150.2513-0.15210.31351.5416-0.00670.95770.10330.54330.63360.01781.360716.81238.274683.6418
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 7:100)
2X-RAY DIFFRACTION2chain A and (resid 101:268)
3X-RAY DIFFRACTION3chain B and (resid 101:268)
4X-RAY DIFFRACTION4chain B and (resid 7:100)
5X-RAY DIFFRACTION5chain X and (resid 1:1)
6X-RAY DIFFRACTION6chain Z and (resid 1:1)

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