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- PDB-3cjs: Minimal Recognition Complex between PrmA and Ribosomal Protein L11 -

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Basic information

Entry
Database: PDB / ID: 3cjs
TitleMinimal Recognition Complex between PrmA and Ribosomal Protein L11
Components
  • 50S ribosomal protein L11
  • Ribosomal protein L11 methyltransferase
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


protein-lysine N-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / large ribosomal subunit rRNA binding / methylation / cytosolic large ribosomal subunit / structural constituent of ribosome / 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 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 methyltransferase (PrmA) / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / 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, RNA binding domain / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL11 / Ribosomal protein L11 methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0056
Polymers21,8193
Non-polymers1863
Water4,594255
1
A: Ribosomal protein L11 methyltransferase
B: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4895
Polymers14,3022
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-8.7 kcal/mol
Surface area7510 Å2
MethodPISA
2
C: 50S ribosomal protein L11


Theoretical massNumber of molelcules
Total (without water)7,5171
Polymers7,5171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.211, 33.948, 71.090
Angle α, β, γ (deg.)90.00, 131.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribosomal protein L11 methyltransferase / L11 Mtase


Mass: 6785.558 Da / Num. of mol.: 1 / Fragment: N-Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: prmA / Plasmid: pET26b / 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: 7516.837 Da / Num. of mol.: 2 / Fragment: N-Terminal Domain
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 22% w/v PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: Sep 15, 2006
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: 1.37→30 Å / Num. obs: 37200 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.5
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3269 / % possible all: 84.7

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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: 1.37→25.72 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.874 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20601 1849 5 %RANDOM
Rwork0.18034 ---
obs0.18166 35338 95.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.711 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.02 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.37→25.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 12 255 1752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221511
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9582058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25824.5151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.36815208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.937155
X-RAY DIFFRACTIONr_chiral_restr0.0840.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021142
X-RAY DIFFRACTIONr_nbd_refined0.20.2762
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2185
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.261
X-RAY DIFFRACTIONr_mcbond_it0.7081.51003
X-RAY DIFFRACTIONr_mcangle_it1.15121576
X-RAY DIFFRACTIONr_scbond_it1.6373589
X-RAY DIFFRACTIONr_scangle_it2.3454.5482
LS refinement shellResolution: 1.37→1.403 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 112 -
Rwork0.248 2232 -
obs-2232 81.67 %
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)
11.4459-0.7907-0.33085.04010.10011.07540.06770.02550.1192-0.3011-0.03750.15780.00840.0268-0.0302-0.04640.0102-0.017-0.0553-0.005-0.019814.5037-10.988720.8493
22.34340.55560.71651.48380.27441.17560.0258-0.1272-0.02950.0251-0.04920.15520.027-0.03690.0234-0.05840.00070.0078-0.0583-0.0033-0.029714.86935.908427.2908
31.3538-0.65232.01741.0151-1.32065.8011-0.08670.1123-0.01440.24090.10610.01790.1711-0.1802-0.01940.0980.01530.02990.07540.0135-0.072314.0196-15.3145-1.2123
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 541 - 54
2X-RAY DIFFRACTION2BB1 - 721 - 72
3X-RAY DIFFRACTION3CC3 - 703 - 70

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