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- PDB-2nxc: Apo-form of T. thermophilus ribosomal protein L11 methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 2nxc
TitleApo-form of T. thermophilus ribosomal protein L11 methyltransferase (PrmA)
ComponentsRibosomal protein L11 methyltransferase
KeywordsTRANSFERASE / TRANSFERASE S-Adenosly-L-Methionine dependent methyltransferase posttranslational modification
Function / homology
Function and homology information


histone methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1350 / : / Ribosomal protein L11 methyltransferase / Sun protein; domain 3 / Ribosomal protein L11 methyltransferase (PrmA) / Vaccinia Virus protein VP39 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1350 / : / Ribosomal protein L11 methyltransferase / Sun protein; domain 3 / Ribosomal protein L11 methyltransferase (PrmA) / Vaccinia Virus protein VP39 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Plaits / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosomal protein L11 methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsDemirci, H. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
CitationJournal: Embo J. / Year: 2007
Title: Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA.
Authors: Demirci, H. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
History
DepositionNov 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal protein L11 methyltransferase


Theoretical massNumber of molelcules
Total (without water)27,6621
Polymers27,6621
Non-polymers00
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.521, 76.557, 61.878
Angle α, β, γ (deg.)90.00, 130.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-347-

HOH

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Components

#1: Protein Ribosomal protein L11 methyltransferase / 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 Star (DE3)
References: UniProt: Q84BQ9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 298 K / Method: sitting-drop vapor diffusion, microseeding / pH: 6.8
Details: 700mM ammonium sulfate, 4%v/v Dioxane, 220mM Hexanediol, 20mM MES, pH 6.8, sitting-drop vapor diffusion and microseeding, temperature 298K

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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 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.59→30 Å / Num. obs: 37520 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.96
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3532 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ufk

1ufk


Resolution: 1.59→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.435 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22405 1889 5 %RANDOM
Rwork0.19229 ---
obs0.1939 35627 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.963 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0.71 Å2
2--1.21 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.59→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 0 168 2091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221978
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9842698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0065247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07922.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03315300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2761518
X-RAY DIFFRACTIONr_chiral_restr0.1190.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021542
X-RAY DIFFRACTIONr_nbd_refined0.2160.2877
X-RAY DIFFRACTIONr_nbtor_refined0.310.21319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.219
X-RAY DIFFRACTIONr_mcbond_it0.9291.51266
X-RAY DIFFRACTIONr_mcangle_it1.50721961
X-RAY DIFFRACTIONr_scbond_it2.5233829
X-RAY DIFFRACTIONr_scangle_it3.9674.5737
LS refinement shellResolution: 1.591→1.632 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 128 -
Rwork0.257 2422 -
obs-2422 88.91 %
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)
12.5510.98850.10771.0246-0.1661.6256-0.0534-0.0347-0.1127-0.15020.0929-0.04130.0350.0333-0.0396-0.0456-0.0146-0.0210.0177-0.0198-0.0269-1.977-28.9966-8.7658
28.2342-1.0906-8.28662.11392.395814.75540.19160.3845-0.05-0.1275-0.05380.0944-1.075-0.482-0.13780.04960.06040.0314-0.10450.0119-0.0023-4.3565-12.5756-2.6088
30.65840.0796-0.02410.31420.38841.03720.07540.0596-0.0064-0.00390.02570.0014-0.02330.1263-0.1011-0.01670.02080.0083-0.011-0.0137-0.0227-10.482310.091812.8229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 541 - 54
2X-RAY DIFFRACTION2AA55 - 6655 - 66
3X-RAY DIFFRACTION3AA67 - 25467 - 254

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