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- PDB-1x7p: Crystal structure of the SpoU Methyltransferase AviRb from Strept... -

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Basic information

Entry
Database: PDB / ID: 1x7p
TitleCrystal structure of the SpoU Methyltransferase AviRb from Streptomyces viridochromogenes in complex with the cofactor AdoMet
ComponentsrRNA methyltransferase
KeywordsTRANSFERASE / SpoU / C-terminal knot / bound Cofactor AdoMet
Function / homology
Function and homology information


23S rRNA (uridine2479-2'-O)-methyltransferase / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA methylation / methylation / response to antibiotic / RNA binding
Similarity search - Function
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 ...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 (uridine(2479)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesStreptomyces viridochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMosbacher, T.G. / Bechthold, A. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure and function of the antibiotic resistance-mediating methyltransferase AviRb from Streptomyces viridochromogenes
Authors: Mosbacher, T.G. / Bechthold, A. / Schulz, G.E.
History
DepositionAug 16, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 16, 2014Group: Experimental preparation
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 methyltransferase
B: rRNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3004
Polymers62,5032
Non-polymers7972
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-12 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.881, 76.881, 209.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsbiological dimer in asymmetric unit

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Components

#1: Protein rRNA methyltransferase / AviRb


Mass: 31251.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces viridochromogenes (bacteria)
Plasmid: pGEX 4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3)
References: UniProt: Q9F5K6, Transferases; Transferring one-carbon groups; Methyltransferases
#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.: 83 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: PEG 300, MES, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9762 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.55→25 Å / Num. obs: 21375 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 55.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.076 / Net I/σ(I): 18.8
Reflection shellResolution: 2.55→2.68 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 9.671 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.536 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25653 1067 5 %RANDOM
Rwork0.202 ---
obs0.20477 20283 100 %-
all-20283 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.55→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3955 0 54 83 4092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214096
X-RAY DIFFRACTIONr_bond_other_d0.0020.023806
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9715583
X-RAY DIFFRACTIONr_angle_other_deg0.8638781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8665515
X-RAY DIFFRACTIONr_chiral_restr0.0770.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024574
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02833
X-RAY DIFFRACTIONr_nbd_refined0.2060.2865
X-RAY DIFFRACTIONr_nbd_other0.220.24298
X-RAY DIFFRACTIONr_nbtor_other0.0850.22550
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.210
X-RAY DIFFRACTIONr_mcbond_it0.4521.52590
X-RAY DIFFRACTIONr_mcangle_it0.85724161
X-RAY DIFFRACTIONr_scbond_it1.31531506
X-RAY DIFFRACTIONr_scangle_it2.3124.51421
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.288 76
Rwork0.24 1442
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)
13.610.8495-1.08373.3989-2.0857.2491-0.0086-0.3526-0.52940.06050.04820.21070.9728-0.1192-0.03960.16230.02750.0620.161-0.03040.209925.761810.4457103.2858
23.86150.208-0.84122.6039-0.85452.08040.02690.14960.295-0.06980.0091-0.12-0.05940.1341-0.0360.04820.00890.010.0635-0.04780.067845.012222.321486.0701
34.93390.41042.9583.3467-1.15227.48950.02420.2204-0.7095-0.58760.44060.63751.5479-0.9786-0.46470.8106-0.29070.00270.321-0.01970.454143.8779-11.55772.9946
43.77030.64320.33734.0231-0.07832.8477-0.0701-0.5378-0.35940.4166-0.0536-0.19480.5580.26570.12370.2020.0840.03580.19760.04590.127759.4522.157592.0898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA18 - 12018 - 120
2X-RAY DIFFRACTION2AA121 - 282121 - 282
3X-RAY DIFFRACTION3BB19 - 6519 - 65
4X-RAY DIFFRACTION3BB68 - 9468 - 94
5X-RAY DIFFRACTION3BB103 - 120103 - 120
6X-RAY DIFFRACTION4BB121 - 281121 - 281

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