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- PDB-1o9g: rRNA methyltransferase aviRa from Streptomyces viridochromogenes ... -

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Basic information

Entry
Database: PDB / ID: 1o9g
TitlerRNA methyltransferase aviRa from Streptomyces viridochromogenes at 1.5A
ComponentsRRNA METHYLTRANSFERASE
KeywordsTRANSFERASE / ANTIBIOTIC RESISTANCE / RRNA-METHYLTRANSFERASE / SE-MAD
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 / SYNCHROTRON / MAD / Resolution: 1.5 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 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RRNA METHYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)26,8331
Polymers26,8331
Non-polymers00
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.362, 47.320, 63.385
Angle α, β, γ (deg.)90.00, 99.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RRNA METHYLTRANSFERASE


Mass: 26833.492 Da / Num. of mol.: 1 / Mutation: YES
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): B834 / Variant (production host): SE-MET / References: UniProt: Q9F5K5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION ILE 11 MET, ARG 190 GLY AND LEU 239 MET. ALSO SEE REMARK 999 FOR MORE DETAILS ...ENGINEERED MUTATION ILE 11 MET, ARG 190 GLY AND LEU 239 MET. ALSO SEE REMARK 999 FOR MORE DETAILS ON THE SECOND ENGINEERED MUTATION.
Has protein modificationY
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 ERTHWEGQVPGQPVAG BY DNA SEQUENCING AND STRUCTURAL STUDIES, RESULTING IN THE CONFLICTS SHOWN IN THE SEQADV RECORDS BELOW.IN ADDITION,RESIDUE 190, WHICH HAS BEEN PROVIDED BY THE DEPOSITORS AS AS AN ALANINE, HAS BEEN ENGINEERED TO A GLYCINE, AS 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 Å3/Da / Density % sol: 39 %
Crystal growpH: 6.9 / Details: PEG 20000 9%, MES 6.6, pH 6.90
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9774
DetectorDate: Sep 8, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.5→37.8 Å / Num. obs: 64711 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rsym value: 0.034 / Net I/σ(I): 38.7
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 6.6 / Rsym value: 0.2 / % possible all: 90
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 15 Å / % possible obs: 97 % / Redundancy: 4.3 % / Num. measured all: 289006 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 90 % / Redundancy: 3.4 % / Num. unique obs: 1482 / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.6

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→37.8 Å / SU B: 1.232 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R Free: 0.082 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1288 3.9 %RANDOM
Rwork0.169 ---
obs0.17 31681 96.5 %-
Displacement parametersBiso mean: 9.096 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.01 Å2
2--0.77 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 0 334 2201
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 25 Å / Num. reflection obs: 33212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.012
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.4

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