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- PDB-3cjr: Ribosomal protein L11 methyltransferase (PrmA) in complex with ri... -

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Basic information

Entry
Database: PDB / ID: 3cjr
TitleRibosomal protein L11 methyltransferase (PrmA) in complex with ribosomal protein L11 (K39A) and inhibitor Sinefungin.
Components
  • 50S ribosomal protein L11
  • Ribosomal protein L11 methyltransferaseRibosome
KeywordsTRANSFERASE/RIBOSOMAL PROTEIN / S-Adenosyl-L-Methionine dependent methyltransferase / post-translational modification / multi-specific trimethylation / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / TRANSFERASE-RIBOSOMAL PROTEIN COMPLEX
Function / homology
Function and homology information


histone methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / large ribosomal subunit rRNA binding / methylation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm
Similarity search - Function
Ribosomal protein L11 methyltransferase / Sun protein; domain 3 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11 methyltransferase (PrmA) / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal ...Ribosomal protein L11 methyltransferase / Sun protein; domain 3 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L11 methyltransferase (PrmA) / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Vaccinia Virus protein VP39 / Arc Repressor Mutant, subunit A / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / Large ribosomal subunit protein uL11 / Ribosomal protein L11 methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDemirci, H. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
CitationJournal: Structure / Year: 2008
Title: Multiple-Site Trimethylation of Ribosomal Protein L11 by the PrmA Methyltransferase.
Authors: Demirci, H. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
History
DepositionMar 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal protein L11 methyltransferase
B: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5113
Polymers43,1302
Non-polymers3811
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-15 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.742, 132.742, 46.056
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Ribosomal protein L11 methyltransferase / Ribosome / L11 Mtase


Mass: 27661.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: prmA / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Star
References: UniProt: Q84BQ9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein 50S ribosomal protein L11 /


Mass: 15468.010 Da / Num. of mol.: 1 / Mutation: K39A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rplK, rpl11 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) prmA::TC / References: UniProt: P36238
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 8.5
Details: 170 mM sodium acetate trihydrate, 85 mM TRIS-HCl, 25.5 (w/v) PEG 4000, 15% (v/v) glycerol, 1 mM Sinefungin, pH 8.5, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2007
Details: Variable vertical and fixed horizontal slits. KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit ...Details: Variable vertical and fixed horizontal slits. KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit beam condition. Located ~18 m from source and ~6 m from sample position. Mirror system consisting of two vertically stacked, fused silica, spherical mirrors, to provide vertical focusing and harmonic rejection. One of the mirrors is rhodium coated and the other is uncoated. Located ~19.7 m from source.
RadiationMonochromator: KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit beam condition. Located ~18 m from source ...Monochromator: KOHZU double crystal monochromator with a water-cooled flat first crystal and a sagittally focused second crystal positioned for a fixed exit beam condition. Located ~18 m from source and ~6 m from sample position.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 27841 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5621 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2NXC, 2NXN

2nxc

2nxn


Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 9.554 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27695 1491 5.1 %RANDOM
Rwork0.21322 ---
obs0.21636 27841 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.919 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.17 Å20 Å2
2---0.33 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 27 328 3146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222881
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.9933927
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1765363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.56622.936109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5915444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4971522
X-RAY DIFFRACTIONr_chiral_restr0.0670.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022185
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1770.21284
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21924
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3141.51881
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.55722919
X-RAY DIFFRACTIONr_scbond_it0.5831157
X-RAY DIFFRACTIONr_scangle_it0.9714.51008
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 104 -
Rwork0.267 2035 -
obs-2035 99.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.42-2.63820.754314.6259-3.74918.8551-0.2243-1.34990.55262.29380.4231.4962-1.0932-0.6329-0.19870.04720.07520.5063-0.018-0.2210.049415.1242-33.799314.2761
20.97130.02310.17271.7142-0.13031.2331-0.02720.008-0.01830.05140.00410.147-0.0334-0.15520.0232-0.0705-0.0080.0016-0.0101-0.0233-0.058750.2902-38.09150.3797
35.68250.8741-1.00437.4822-0.08934.26440.15-0.52740.24280.2484-0.0930.4467-0.133-0.1551-0.0571-0.2526-0.02880.0443-0.0595-0.1025-0.058824.9217-40.89350.6663
413.47990.3593.910819.74553.912214.25030.06540.91570.425-0.9318-0.01190.22420.2066-0.2233-0.05340.01120.04050.0779-0.00310.01910.01513.0327-18.2487-4.1355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 541 - 54
2X-RAY DIFFRACTION2AA67 - 25467 - 254
3X-RAY DIFFRACTION3BB1 - 701 - 70
4X-RAY DIFFRACTION4BB73 - 13773 - 137

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