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- PDB-4auk: Crystal structure of C2498 2'-O-ribose methyltransferase RlmM fro... -

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Basic information

Entry
Database: PDB / ID: 4auk
TitleCrystal structure of C2498 2'-O-ribose methyltransferase RlmM from Escherichia coli
ComponentsRIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
KeywordsTRANSFERASE / YGDE
Function / homology
Function and homology information


23S rRNA (cytidine2498-2'-O)-methyltransferase / rRNA (cytosine-2'-O-)-methyltransferase activity / rRNA processing / cytoplasm
Similarity search - Function
THUMP fold - #20 / Alpha-Beta Plaits - #2810 / Ribosomal RNA large subunit methyltransferase M / RlmM ferredoxin-like domain / : / RlmM ferredoxin-like domain / Ribosomal RNA large subunit methyltransferase M, N-terminal / THUMP fold / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase ...THUMP fold - #20 / Alpha-Beta Plaits - #2810 / Ribosomal RNA large subunit methyltransferase M / RlmM ferredoxin-like domain / : / RlmM ferredoxin-like domain / Ribosomal RNA large subunit methyltransferase M, N-terminal / THUMP fold / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Vaccinia Virus protein VP39 / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / L(+)-TARTARIC ACID / Ribosomal RNA large subunit methyltransferase M
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPunekar, A.S. / Shepherd, T.R. / Liljeruhm, J. / Forster, A.C. / Selmer, M.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal Structure of Rlmm, the 2'O-Ribose Methyltransferase for C2498 of Escherichia Coli 23S Rrna.
Authors: Punekar, A.S. / Shepherd, T.R. / Liljeruhm, J. / Forster, A.C. / Selmer, M.
History
DepositionMay 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Nov 14, 2012Group: Database references
Revision 1.4Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
B: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,67932
Polymers86,2492
Non-polymers2,43130
Water9,944552
1
A: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,81421
Polymers43,1241
Non-polymers1,69020
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,86511
Polymers43,1241
Non-polymers74110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.800, 132.800, 41.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2589, 0.9659, 0.0092), (0.9659, -0.2588, -0.0098), (-0.0071, 0.0114, -0.9999)
Vector: 61.4002, -79.7765, 0.6797)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M / 23S RRNA (CYTIDINE2498-2'-O)-METHYLTRANSFERASE / 23S RRNA 2'-O-RIBOSE METHYLTRANSFERASE RLMM


Mass: 43124.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PEXP5-CT/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0ADR6, 23S rRNA (cytidine2498-2'-O)-methyltransferase

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Non-polymers , 8 types, 582 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYZES THE 2'-O-METHYLATION AT NUCLEOTIDE C2498 IN 23S RRNA OF ESCHERICHIA COLI
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: 2.46 Å3/Da / Density % sol: 49.93 % / Description: NONE
Crystal growpH: 8.5
Details: 0.3 M AMMONIUM TARTRATE DIBASIC PH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04
DetectorType: MARRESEARCH MAR165 / Detector: CCD / Date: Dec 15, 2011 / Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.9→20.1 Å / Num. obs: 64264 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 18.49 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.72
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.57 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.42 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ATN

4atn


Resolution: 1.9→20.118 Å / SU ML: 0.25 / σ(F): 2 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 3212 5 %
Rwork0.1639 --
obs0.1661 64264 99.75 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.638 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 22.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.0297 Å20 Å20 Å2
2--0.0297 Å20 Å2
3----0.0594 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5743 0 157 552 6452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166096
X-RAY DIFFRACTIONf_angle_d1.5678221
X-RAY DIFFRACTIONf_dihedral_angle_d14.2832293
X-RAY DIFFRACTIONf_chiral_restr0.109860
X-RAY DIFFRACTIONf_plane_restr0.0071057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9003-1.92860.40511310.33072517X-RAY DIFFRACTION95
1.9286-1.95870.28391420.21472685X-RAY DIFFRACTION100
1.9587-1.99080.2591390.19132639X-RAY DIFFRACTION100
1.9908-2.02510.21791380.17292628X-RAY DIFFRACTION100
2.0251-2.06190.2251410.17232688X-RAY DIFFRACTION100
2.0619-2.10150.24071400.1742659X-RAY DIFFRACTION100
2.1015-2.14440.22171420.16692692X-RAY DIFFRACTION100
2.1444-2.19090.22331380.16092629X-RAY DIFFRACTION100
2.1909-2.24180.23921410.16252665X-RAY DIFFRACTION100
2.2418-2.29780.23371390.15792655X-RAY DIFFRACTION100
2.2978-2.35990.20551410.16652677X-RAY DIFFRACTION100
2.3599-2.42920.21561400.16722650X-RAY DIFFRACTION100
2.4292-2.50740.22761390.17362643X-RAY DIFFRACTION100
2.5074-2.59690.22241420.17112696X-RAY DIFFRACTION100
2.5969-2.70060.21621380.17412633X-RAY DIFFRACTION100
2.7006-2.82320.241400.17562650X-RAY DIFFRACTION100
2.8232-2.97160.20111410.17562690X-RAY DIFFRACTION100
2.9716-3.15720.21161410.16512672X-RAY DIFFRACTION100
3.1572-3.39980.17621400.15792665X-RAY DIFFRACTION100
3.3998-3.740.2111400.15152647X-RAY DIFFRACTION100
3.74-4.27670.17191390.13612640X-RAY DIFFRACTION100
4.2767-5.37110.14721400.12912670X-RAY DIFFRACTION100
5.3711-20.11930.16551400.15832662X-RAY DIFFRACTION100

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