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- PDB-3egv: Ribosomal protein L11 methyltransferase (PrmA) in complex with tr... -

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Basic information

Entry
Database: PDB / ID: 3egv
TitleRibosomal protein L11 methyltransferase (PrmA) in complex with trimethylated ribosomal protein L11
Components
  • 50S ribosomal protein L11
  • Ribosomal protein L11 methyltransferase
KeywordsTRANSFERASE/RIBOSOMAL PROTEIN / post-translational modification / multiple methyltransferase / Methyltransferase / Transferase / Methylation / 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. / Vaccinia Virus protein VP39 ...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. / Vaccinia Virus protein VP39 / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / S-ADENOSYL-L-HOMOCYSTEINE / Large ribosomal subunit protein uL11 / Ribosomal protein L11 methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
DepositionSep 11, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionSep 23, 2008ID: 3CJU
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 18, 2017Group: Non-polymer description
Revision 1.3Mar 1, 2017Group: Non-polymer description
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / 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 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_polymer_linkage / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_polymer_linkage.auth_atom_id_1 / _struct_conn.ptnr1_label_atom_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0889
Polymers43,1732
Non-polymers9157
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-38 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.547, 134.547, 48.944
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ribosomal protein L11 methyltransferase / L11 Mtase


Mass: 27661.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cytoplasm / Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: prmA, TTHA0656 / 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: 15511.098 Da / Num. of mol.: 1 / Mutation: K16A
Source method: isolated from a genetically manipulated source
Details: cytoplasm / Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: rpl11, rplK, TTHA0247 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 PrmA::tc / References: UniProt: Q5SLP6

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Non-polymers , 5 types, 422 molecules

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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 58.64 %
Crystal growTemperature: 277 K / Method: microbatch technique under oil / pH: 6.5
Details: 160 mM calcium acetate hydrate, 80 mM sodium cacodylate, 14.4% w/v PEG8000, 20% v/v glycerol, 4mM AdoMet, pH 6.5, microbatch technique under oil, temperature 277.0K

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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: 1.75→30 Å / Num. obs: 48051 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2 / Num. unique all: 9414 / % possible all: 93.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 2NXC, 2NXN

2nxc

2nxn


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.55 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21332 2577 5.1 %RANDOM
Rwork0.18251 ---
obs0.18416 48051 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.628 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 52 415 2997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222648
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5032.0023610
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8885329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.81922.913103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06215389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0811519
X-RAY DIFFRACTIONr_chiral_restr0.1020.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022015
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21261
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21727
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2296
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7621.51670
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18722644
X-RAY DIFFRACTIONr_scbond_it2.00231095
X-RAY DIFFRACTIONr_scangle_it3.1734.5966
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 198 -
Rwork0.29 3478 -
obs-3478 98.45 %
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)
17.2815-2.4438-2.19224.31611.85741.969-0.0103-0.05990.6951-0.14420.3339-0.6175-0.13320.4539-0.3236-0.1986-0.04450.12180.0207-0.17280.0516-11.5454-39.0477-6.5994
21.7067-0.32410.26451.5108-0.1361.3502-0.1283-0.12130.070.11640.1152-0.1628-0.1013-0.01260.0131-0.04790.0308-0.0149-0.0471-0.04-0.0793-52.0935-35.942111.2867
35.2127-0.1398-2.11030.97720.55942.86850.08310.32790.4781-0.19140.0818-0.2154-0.13060.011-0.1649-0.10410.00540.0609-0.0353-0.0140.0427-29.7161-36.8826-4.3478
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 54
2X-RAY DIFFRACTION2A67 - 254
3X-RAY DIFFRACTION3B2 - 70

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