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- PDB-3cjq: Ribosomal protein L11 methyltransferase (PrmA) in complex with di... -

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Basic information

Entry
Database: PDB / ID: 3cjq
TitleRibosomal protein L11 methyltransferase (PrmA) in complex with dimethylated ribosomal protein L11 in space group P212121
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 / cytosol
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, 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, RNA binding domain / Ribosomal protein L11/L12 / 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
N,N-dimethyl-L-methionine / IODIDE ION / S-ADENOSYL-L-HOMOCYSTEINE / Large ribosomal subunit protein uL11 / Ribosomal protein L11 methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_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
D: Ribosomal protein L11 methyltransferase
E: 50S ribosomal protein L11
G: Ribosomal protein L11 methyltransferase
H: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,93514
Polymers128,9966
Non-polymers1,9398
Water4,342241
1
A: Ribosomal protein L11 methyltransferase
B: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6875
Polymers42,9992
Non-polymers6893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-22.7 kcal/mol
Surface area17730 Å2
MethodPISA
2
D: Ribosomal protein L11 methyltransferase
E: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5604
Polymers42,9992
Non-polymers5622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-20.5 kcal/mol
Surface area17110 Å2
MethodPISA
3
G: Ribosomal protein L11 methyltransferase
H: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6875
Polymers42,9992
Non-polymers6893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-22.4 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.526, 164.976, 180.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31G
41A
51D
61G
12B
22E
32H
42B
52E
62H

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDEnd label seq-ID
111METMETVALVALAA1 - 541 - 54
211METMETVALVALDC1 - 541 - 54
311METMETVALVALGE1 - 541 - 54
421LEULEUARGARGAA67 - 25467 - 254
521LEULEUARGARGDC67 - 25467 - 254
621LEULEUARGARGGE67 - 25467 - 254
1122MM2MMLYSLYSBI - B1 - 7069
2122MM2MMLYSLYSEK - D1 - 7069
3122MM2MMLYSLYSHN - F1 - 7069
422PROPROSERSERBB73 - 13072 - 129
522PROPROSERSERED73 - 13072 - 129
622PROPROSERSERHF73 - 13072 - 129

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 6 molecules ADGBEH

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


Mass: 27661.807 Da / Num. of mol.: 3
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: 15336.812 Da / Num. of mol.: 3 / 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

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Non-polymers , 4 types, 249 molecules

#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-2MM / N,N-dimethyl-L-methionine


Mass: 177.264 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H15NO2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 7.5
Details: 100 mM HEPES, 10% w/v PEG8000, 8% v/v ethylene glycol, pH 7.5, 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: Nov 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: 2.7→30 Å / Num. obs: 45471 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.92 / Num. unique all: 4188 / % possible all: 93.1

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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: 2.7→29.09 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.899 / SU B: 22.053 / SU ML: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.683 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27119 2207 5.1 %RANDOM
Rwork0.20162 ---
obs0.20507 40969 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8442 0 110 241 8793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0228770
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1071.99211953
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96651103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86722.857336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.204151330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9671566
X-RAY DIFFRACTIONr_chiral_restr0.130.21336
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026656
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.23766
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.25559
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2351
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0541.55628
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65328869
X-RAY DIFFRACTIONr_scbond_it2.6333556
X-RAY DIFFRACTIONr_scangle_it4.0254.53084
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1836medium positional0.460.5
12D1836medium positional0.430.5
13G1836medium positional0.480.5
21B761medium positional0.820.5
22E761medium positional1.250.5
23H761medium positional0.930.5
11A1836medium thermal1.212
12D1836medium thermal1.432
13G1836medium thermal1.252
21B761medium thermal0.842
22E761medium thermal1.042
23H761medium thermal0.992
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 173 -
Rwork0.283 2895 -
obs-2895 99.84 %
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)
14.6124-3.0564-0.488611.36770.64595.40360.29640.346-0.0709-0.8441-0.38440.0321-0.1591-0.02770.0881-0.11010.11240.0172-0.5106-0.0019-0.12810.222254.7282-64.5372
23.1546-0.57040.56022.4319-0.4912.15550.1034-0.12270.30470.0292-0.0909-0.0849-0.23540.2097-0.0125-0.1005-0.01870.076-0.2248-0.0178-0.019621.888518.6076-51.7182
36.5684-4.1414-1.07798.86210.2993.74520.30030.0057-0.22160.0535-0.19840.6126-0.1526-0.2828-0.1018-0.01390.03540.0733-0.47270.0689-0.01124.134538.1067-59.1252
411.1663-2.519714.74366.4375-1.597619.97650.46-0.2222-1.10631.07850.25441.10181.19990.6106-0.71450.2984-0.24680.19540.12160.14340.3254-13.440151.899-39.7264
55.2795-0.0295-2.41565.54882.42087.0062-0.3193-0.6071-0.60760.24380.13010.05511.035-0.23310.1892-0.1061-0.06560.05760.19540.1846-0.4564-15.7604-11.25941.3683
62.69350.1022-0.35161.99480.24312.92710.0936-0.188-0.18070.0793-0.0888-0.20580.0417-0.0204-0.0048-0.1317-0.01520.0406-0.16350.0709-0.11934.8789-3.8598-36.8004
73.65741.196-2.88362.4834-1.2567.17280.0419-0.1929-0.0140.00370.01180.15580.5565-0.6959-0.0537-0.0986-0.1038-0.00880.01150.0661-0.4391-12.8219-7.59-15.9091
81.9126-4.4913-3.352719.0824-2.466318.40090.3465-0.0108-0.66910.1050.1020.01591.56981.2637-0.44850.2808-0.18110.08850.1521-0.03920.2742-26.45-32.5932-8.2362
92.45120.5643-0.43471.08762.12085.2276-0.04060.6465-0.8828-0.53210.27150.3320.8634-0.424-0.23090.5074-0.165-0.24590.4256-0.47410.576218.6744-34.6101-89.7608
103.172-0.20130.08612.99320.2712.63660.04130.4216-0.2598-0.0634-0.0410.22840.13760.0742-0.0004-0.17520.00650.0121-0.0518-0.1153-0.14639.3182-5.4669-63.7361
113.4466-0.33821.812.0958-0.59196.40280.18270.4987-0.5801-0.41810.11980.43420.3952-0.7596-0.30240.0618-0.1271-0.14140.0792-0.36050.249521.8037-21.6205-77.6064
123.36471.12471.59983.35220.67880.76760.0707-0.30810.44310.3843-0.02270.19490.1105-0.0941-0.04811.3196-0.03970.06671.18630.08441.09584.7877-11.4241-100.1629
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 DIFFRACTION3BB2 - 701 - 69
4X-RAY DIFFRACTION4BB99 - 14098 - 139
5X-RAY DIFFRACTION5DC1 - 541 - 54
6X-RAY DIFFRACTION6DC67 - 25467 - 254
7X-RAY DIFFRACTION7ED2 - 701 - 69
8X-RAY DIFFRACTION8ED99 - 14098 - 139
9X-RAY DIFFRACTION9GE1 - 541 - 54
10X-RAY DIFFRACTION10GE67 - 25467 - 254
11X-RAY DIFFRACTION11HF2 - 701 - 69
12X-RAY DIFFRACTION12HF99 - 14098 - 139

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