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- PDB-1o9h: rRNA methyltransferase aviRa from Streptomyces viridochromogenes ... -

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Basic information

Entry
Database: PDB / ID: 1o9h
TitlerRNA methyltransferase aviRa from Streptomyces viridochromogenes at 2.4A
ComponentsRRNA METHYLTRANSFERASE
KeywordsTRANSFERASE / ANTIBIOTIC RESISTANCE / RRNA-METHYLTRANSFERASE
Function / homology
Function and homology information


23S rRNA (guanine2535-N1)-methyltransferase / rRNA (guanine-N1-)-methyltransferase activity / rRNA methylation / methylation / response to antibiotic
Similarity search - Function
rRNA methyltransferase AviRa / RRNA methyltransferase AviRa / Helix hairpin bin / Vaccinia Virus protein VP39 / Helix Hairpins / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
23S rRNA (guanine(2535)-N(1))-methyltransferase
Similarity search - Component
Biological speciesSTREPTOMYCES VIRIDOCHROMOGENES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMosbacher, T.G. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of the Avilamycin Resistance-Conferring Methyltransferase Avira from Streptomyces Viridochromogenes
Authors: Mosbacher, T.G. / Bechthold, A. / Schulz, G.E.
History
DepositionDec 13, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RRNA METHYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)26,6711
Polymers26,6711
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.098, 48.937, 63.714
Angle α, β, γ (deg.)90.00, 99.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RRNA METHYLTRANSFERASE


Mass: 26670.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES VIRIDOCHROMOGENES (bacteria)
Plasmid: PRSETB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F5K5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE IN DATABASE INCORRECT FROM RESIDUE 180 TO 195. THE SWISS-PROT ACCESSION Q9F5K5 HAS THE ...SEQUENCE IN DATABASE INCORRECT FROM RESIDUE 180 TO 195. THE SWISS-PROT ACCESSION Q9F5K5 HAS THE SEQUENCE SARTGKGRCPRSRWRA FOR RESIDUES 180-195, WHEREAS THE DEPOSITORS HAVE DETERMINED THE SEQUENCE TO BE ERTHWEGQVPAQPVAG, RESULTING IN THE CONFLICTS SHOWN IN THE SEQADV RECORDS BELOW.

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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: 2.14 Å3/Da / Density % sol: 39 %
Crystal growpH: 6.6 / Details: MES 6.6,PEG 20K 11%, pH 6.60
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / PH range low: 6.9 / PH range high: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
2100 mMMES1reservoirpH6.6-6.9
36-8 %(w/v)PEG200001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418
DetectorType: BRUKER / Detector: AREA DETECTOR / Date: Jan 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→26.4 Å / Num. obs: 8039 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 38.7
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 3.2 / % possible all: 90
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Num. obs: 8093 / % possible obs: 91 % / Redundancy: 2.3 % / Num. measured all: 19577 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 91 % / Redundancy: 1.5 % / Num. unique obs: 921 / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9G

1o9g


Resolution: 2.4→26.44 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.11 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 2.091 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 382 4.7 %RANDOM
Rwork0.209 ---
obs0.211 7709 90.1 %-
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: 49.48 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å2-0.55 Å2
2--2.77 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 0 29 1897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211905
X-RAY DIFFRACTIONr_bond_other_d0.0020.021854
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9872598
X-RAY DIFFRACTIONr_angle_other_deg0.77934266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9815248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022135
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02388
X-RAY DIFFRACTIONr_nbd_refined0.1960.2417
X-RAY DIFFRACTIONr_nbd_other0.2180.22195
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21205
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0650.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9121.51248
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70321997
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.663657
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1124.5601
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
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.327 21
Rwork0.224 437
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Num. reflection obs: 8093
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.19

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