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- PDB-3nk7: Structure of the Nosiheptide-resistance methyltransferase S-adeno... -

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Basic information

Entry
Database: PDB / ID: 3nk7
TitleStructure of the Nosiheptide-resistance methyltransferase S-adenosyl-L-methionine Complex
Components23S rRNA methyltransferase
KeywordsTRANSFERASE / Nosiheptide / Nosiheptide-resistance methyltransferase / 23S rRNA methyltransferase / SAM
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 actuosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Nov 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

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Assembly

Deposited unit
A: 23S rRNA methyltransferase
B: 23S rRNA methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9594
Polymers59,1622
Non-polymers7972
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-9 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.651, 69.211, 64.444
Angle α, β, γ (deg.)90.00, 117.56, 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: 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.: 139 / 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: 2.13 Å3/Da / Density % sol: 42.17 %
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: 0.9794 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: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 28998 / Num. obs: 28585 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 37.64 Å2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 8.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NK6

3nk6


Resolution: 2.1→32.18 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.805 / SU ML: 0.36 / σ(F): 0.12 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 1448 5.07 %
Rwork0.1957 27137 -
obs0.1987 28585 97.8 %
all-28998 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.243 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 202.21 Å2 / Biso mean: 53.7181 Å2 / Biso min: 15.98 Å2
Baniso -1Baniso -2Baniso -3
1-6.4737 Å2-0 Å21.657 Å2
2---2.0051 Å20 Å2
3----4.4685 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3969 0 54 139 4162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134071
X-RAY DIFFRACTIONf_angle_d1.5015521
X-RAY DIFFRACTIONf_dihedral_angle_d19.2671523
X-RAY DIFFRACTIONf_chiral_restr0.094679
X-RAY DIFFRACTIONf_plane_restr0.007715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0968-2.17180.31331400.23692595X-RAY DIFFRACTION94
2.1718-2.25870.28461650.22092593X-RAY DIFFRACTION96
2.2587-2.36150.32151380.19732727X-RAY DIFFRACTION97
2.3615-2.48590.24551460.20462704X-RAY DIFFRACTION99
2.4859-2.64160.32231320.19982758X-RAY DIFFRACTION99
2.6416-2.84540.30891510.21442733X-RAY DIFFRACTION99
2.8454-3.13160.26061540.21162764X-RAY DIFFRACTION100
3.1316-3.58420.25841400.18592791X-RAY DIFFRACTION100
3.5842-4.51370.19491430.16682808X-RAY DIFFRACTION100
4.5137-500.23441390.18772664X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 8.6106 Å / Origin y: 7.9399 Å / Origin z: 14.0746 Å
111213212223313233
T0.1541 Å2-0.0001 Å20.0313 Å2-0.1321 Å20.0067 Å2--0.1513 Å2
L1.7795 °2-0.2277 °2-0.4391 °2-0.6709 °2-0.01 °2--1.1415 °2
S-0.1661 Å °-0.0621 Å °-0.0656 Å °0.0041 Å °0.1143 Å °0.0765 Å °0.0603 Å °-0.0849 Å °0.046 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 770
2X-RAY DIFFRACTION1allB5 - 770
3X-RAY DIFFRACTION1allA - B1 - 350

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