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- PDB-1gz0: 23S RIBOSOMAL RNA G2251 2'O-METHYLTRANSFERASE RLMB -

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Basic information

Entry
Database: PDB / ID: 1gz0
Title23S RIBOSOMAL RNA G2251 2'O-METHYLTRANSFERASE RLMB
ComponentsHYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
KeywordsTRANSFERASE / METHYLTRANSFERASE / 2'O-METHYLTRANSFERASE / KNOT / MONTREAL- KINGSTON BACTERIAL STRUCTURAL GENOMICS INITIATIVE / BSGI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


23S rRNA (guanosine2251-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / rRNA processing / RNA binding / cytoplasm / cytosol
Similarity search - Function
RNA methyltransferase TrmH family / 23S rRNA (guanosine-2-O-)-methyltransferase RlmB / RNA 2'-O ribose methyltransferase substrate binding / RNA 2-O ribose methyltransferase, substrate binding / RNA 2'-O ribose methyltransferase substrate binding / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / Ribosomal protein L30/S12 / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot ...RNA methyltransferase TrmH family / 23S rRNA (guanosine-2-O-)-methyltransferase RlmB / RNA 2'-O ribose methyltransferase substrate binding / RNA 2-O ribose methyltransferase, substrate binding / RNA 2'-O ribose methyltransferase substrate binding / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / Ribosomal protein L30/S12 / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / 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 (guanosine-2'-O-)-methyltransferase RlmB / 23S rRNA (guanosine-2'-O-)-methyltransferase RlmB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsMichel, G. / Cygler, M.
CitationJournal: Structure / Year: 2002
Title: The Structure of the Rlmb 23S Rrna Methyltransferase Reveals a New Methyltransferase Fold with a Unique Knot
Authors: Michel, G. / Sauve, V. / Larocque, R. / Li, Y. / Matte, A. / Cygler, M.
History
DepositionMay 3, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
B: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
C: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
D: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
E: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
F: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
G: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
H: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH


Theoretical massNumber of molelcules
Total (without water)223,5598
Polymers223,5598
Non-polymers00
Water3,189177
1
A: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
F: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH


Theoretical massNumber of molelcules
Total (without water)55,8902
Polymers55,8902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
G: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH


Theoretical massNumber of molelcules
Total (without water)55,8902
Polymers55,8902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
H: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH


Theoretical massNumber of molelcules
Total (without water)55,8902
Polymers55,8902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
E: HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH


Theoretical massNumber of molelcules
Total (without water)55,8902
Polymers55,8902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.478, 132.288, 90.710
Angle α, β, γ (deg.)90.00, 96.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH / METHYLTRANSFERASE


Mass: 27944.881 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MC1061 P3 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DL41(DE3)
References: UniProt: P39290, UniProt: P63177*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHIS-TAG, SELEMETHIONYL PROTEIN. THE RESIDUES NUMBERED FROM -10 TO -1 CORRESPOND TO THE PURIFICATION TAG
Has protein modificationY

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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: 2.249 Å3/Da / Density % sol: 43 %
Crystal growpH: 7.5 / Details: PEG400, TRIS-HCL, pH 7.50
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
220 mMTris-HCl1droppH8.5
3500 mM1dropNaCl
45 %(w/v)glycerol1drop
55 mMdithiothreitol1drop
615 %(v/v)PEG4001reservoir
750 mMTris-HCl1reservoirpH7.5
8440 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: May 17, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→47 Å / Num. obs: 286761 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.06 % / Biso Wilson estimate: 43 Å2 / Net I/σ(I): 23
Reflection shellResolution: 2.5→2.59 Å / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 47 Å / Num. obs: 70653 / Redundancy: 4.06 % / Num. measured all: 286761 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 98.3 % / Rmerge(I) obs: 0.371

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→46.86 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1925218.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 3587 5.1 %RANDOM
Rwork0.231 ---
obs0.231 70381 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.7186 Å2 / ksol: 0.334869 e/Å3
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1--5.95 Å20 Å21.01 Å2
2--5.03 Å20 Å2
3---0.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13776 0 0 177 13953
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 578 5 %
Rwork0.287 11020 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 47 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0084
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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