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- PDB-2nxj: T.thermophilus ribosomal protein L11 methyltransferase (PrmA) in ... -

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Basic information

Entry
Database: PDB / ID: 2nxj
TitleT.thermophilus ribosomal protein L11 methyltransferase (PrmA) in space group P 21 21 2
ComponentsRibosomal protein L11 methyltransferase
KeywordsTRANSFERASE / S-Adenosyl-L-Methionine dependent methyltransferase / postranslational modification
Function / homology
Function and homology information


protein-lysine N-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methylation / cytoplasm
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: 2.3 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 1.0Dec 26, 2006Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Ribosomal protein L11 methyltransferase
B: Ribosomal protein L11 methyltransferase


Theoretical massNumber of molelcules
Total (without water)55,3242
Polymers55,3242
Non-polymers00
Water5,224290
1
A: Ribosomal protein L11 methyltransferase


Theoretical massNumber of molelcules
Total (without water)27,6621
Polymers27,6621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal protein L11 methyltransferase


Theoretical massNumber of molelcules
Total (without water)27,6621
Polymers27,6621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.195, 153.622, 33.255
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ribosomal protein L11 methyltransferase / L11 Mtase


Mass: 27661.807 Da / Num. of mol.: 2
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.: 290 / 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: 2.86 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.7 M Ammonium sulfate, 85 mM HEPES-Na, pH 7.5, 1.7% w/v PEG400, 15% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9797
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 29480 / Num. obs: 28554 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2530 / % possible all: 85.8

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Processing

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

1nxc


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.902 / SU B: 17.687 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27624 1446 5.1 %RANDOM
Rwork0.20783 ---
obs0.21139 27095 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.57 Å2
Baniso -1Baniso -2Baniso -3
1-4.55 Å20 Å20 Å2
2---2.1 Å20 Å2
3----2.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 0 290 4089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223906
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9855326
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0315485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77822.47166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.34415595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2121536
X-RAY DIFFRACTIONr_chiral_restr0.1060.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023030
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21685
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22500
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8361.52488
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4523869
X-RAY DIFFRACTIONr_scbond_it1.96331645
X-RAY DIFFRACTIONr_scangle_it3.1214.51457
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 87 -
Rwork0.267 1742 -
obs-1742 84.64 %
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)
112.4127-2.2253-3.34726.5462-0.76134.81780.06251.03860.7573-0.3805-0.17490.7936-0.4303-0.29410.1124-0.27440.0964-0.1336-0.08670.00610.230661.151351.7736-3.7215
20.2746-0.4535-0.08391.8804-0.0521.4503-0.04160.0170.04860.05920.04180.03230.14410.1002-0.00020.00310.0274-0.005-0.0631-0.0075-0.056328.498422.86830.183
312.06761.67460.85776.6901-2.12985.1158-0.5562-0.8405-2.12630.13130.4111.1780.0458-0.13460.1452-0.42020.10170.1699-0.21850.08390.768662.983236.67445.1931
40.67190.5887-0.66312.9804-1.44152.18140.14060.01240.08180.21320.04970.2486-0.26050.1223-0.19030.0449-0.04690.0483-0.07810.0054-0.081525.659159.8326-1.4553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 541 - 54
2X-RAY DIFFRACTION2AA57 - 25457 - 254
3X-RAY DIFFRACTION3BB1 - 541 - 54
4X-RAY DIFFRACTION4BB62 - 25462 - 254

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