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- PDB-3nk6: Structure of the Nosiheptide-resistance methyltransferase -

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Basic information

Entry
Database: PDB / ID: 3nk6
TitleStructure of the Nosiheptide-resistance methyltransferase
Components23S rRNA methyltransferase
KeywordsTRANSFERASE / Nosiheptide / Nosiheptide-resistance methyltransferase / 23S rRNA methyltransferase
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
23S rRNA (adenosine(1067)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesStreptomyces actuosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsYang, H. / Wang, Z. / Shen, Y. / Wang, P. / Murchie, A. / Xu, Y.
CitationJournal: Biochemistry / Year: 2010
Title: Crystal Structure of the Nosiheptide-Resistance Methyltransferase of Streptomyces actuosus
Authors: Yang, H. / Wang, Z. / Shen, Y. / Wang, P. / Jia, X. / Zhao, L. / Zhou, P. / Gong, R. / Li, Z. / Yang, Y. / Chen, D. / Murchie, A.I.H. / Xu, Y.
History
DepositionJun 18, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 23S rRNA methyltransferase
B: 23S rRNA methyltransferase


Theoretical massNumber of molelcules
Total (without water)59,1622
Polymers59,1622
Non-polymers00
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-11 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.884, 69.203, 64.797
Angle α, β, γ (deg.)90.00, 117.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 23S rRNA methyltransferase / rRNA (ADENOSINE-2'-O-)-METHYLTRANSFERASE / 23S rRNA methylase


Mass: 29580.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces actuosus (bacteria) / Gene: nsr / Plasmid: pETduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P52391, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 43.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.35M ammonium chloride, 24%(w/v) PEG 3350, 0.1M MES, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0055 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0055 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 34122 / Num. obs: 33406 / % possible obs: 97.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 28.18 Å2
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 8 / Num. unique all: 3257 / % possible all: 95.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→33.469 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7935 / SU ML: 0.31 / σ(F): 0.14 / Phase error: 27.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 1677 5.02 %
Rwork0.2013 31729 -
obs0.2039 33406 96.96 %
all-34122 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.153 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 109.74 Å2 / Biso mean: 37.469 Å2 / Biso min: 9.78 Å2
Baniso -1Baniso -2Baniso -3
1--6.7791 Å20 Å2-1.0234 Å2
2---1.5747 Å2-0 Å2
3---8.3538 Å2
Refinement stepCycle: LAST / Resolution: 2→33.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 0 312 4192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083917
X-RAY DIFFRACTIONf_angle_d1.2165308
X-RAY DIFFRACTIONf_dihedral_angle_d17.6431447
X-RAY DIFFRACTIONf_chiral_restr0.077657
X-RAY DIFFRACTIONf_plane_restr0.006693
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0580.28151280.20212330245886
2.058-2.12440.29291340.20542561269594
2.1244-2.20030.27931470.21112573272095
2.2003-2.28840.33551280.21152631275997
2.2884-2.39250.28811410.21592656279797
2.3925-2.51860.29871450.21292636278199
2.5186-2.67640.31291270.22712726285399
2.6764-2.88290.2891460.22562694284099
2.8829-3.17280.25271370.21042704284199
3.1728-3.63150.23391470.196827312878100
3.6315-4.57340.21581500.175327382888100
4.5734-500.20861470.1822749289698

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