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

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Basic information

Entry
Database: PDB / ID: 2nxe
TitleT. thermophilus ribosomal protein L11 methyltransferase (PrmA) in complex with S-Adenosyl-L-Methionine
ComponentsRibosomal protein L11 methyltransferaseRibosome
KeywordsTRANSFERASE / S-Adenosyl-L-Methionine dependent methyltransferase / postranslational modification
Function / homology
Function and homology information


histone 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 / Rossmann fold ...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
S-ADENOSYLMETHIONINE / Ribosomal protein L11 methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 ...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: Ribosomal protein L11 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1204
Polymers55,3242
Non-polymers7972
Water5,242291
1
A: Ribosomal protein L11 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0602
Polymers27,6621
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal protein L11 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0602
Polymers27,6621
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.179, 187.179, 45.189
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Ribosomal protein L11 methyltransferase / Ribosome / 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: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 277 K / pH: 7.5
Details: 190 mM Calcium chloride dihydrate, 95mM HEPES-Na, pH 7.5, 26.6% v/v PEG400, 5% glycerol, 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
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: 1.75→30 Å / Num. all: 59737 / Num. obs: 59391 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 19.13
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5929 / % possible all: 99.5

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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 2NXC

2nxc


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.645 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22396 3002 5.1 %RANDOM
Rwork0.20149 ---
obs0.20265 56389 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.865 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3860 0 54 291 4205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224029
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.9995499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0622.395167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89315601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2511536
X-RAY DIFFRACTIONr_chiral_restr0.1290.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023122
X-RAY DIFFRACTIONr_nbd_refined0.210.21896
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22669
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3820.2302
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.216
X-RAY DIFFRACTIONr_mcbond_it1.0061.52563
X-RAY DIFFRACTIONr_mcangle_it1.52423965
X-RAY DIFFRACTIONr_scbond_it2.36731723
X-RAY DIFFRACTIONr_scangle_it3.5924.51534
LS refinement shellResolution: 1.75→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 250 -
Rwork0.282 4133 -
obs-4133 99.21 %
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)
14.06950.43120.76271.5293-0.47920.67540.03660.4571-0.2453-0.0343-0.01190.02140.1580.4618-0.0247-0.0924-0.00040.03960.2063-0.0737-0.100128.8657-22.850224.5819
21.49170.2871-0.28981.1041-0.32680.3249-0.0149-0.0385-0.10970.0085-0.03870.04840.0167-0.00960.0535-0.0307-0.06090.0663-0.0258-0.0191-0.00692.1859-25.449514.9401
37.469-1.4273-1.34941.650.42732.1125-0.383-0.1104-0.15070.08630.26220.09750.04170.0530.1208-0.0793-0.05470.06390.0411-0.0085-0.070822.5583-17.6885-5.0309
40.9771-0.2248-0.38490.81030.19420.9657-0.0883-0.00220.00470.0560.01580.02980.0533-0.06230.0725-0.0305-0.0070.0139-0.01150.0035-0.044447.9619-7.2631-1.0242
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 531 - 53
2X-RAY DIFFRACTION2AA67 - 25467 - 254
3X-RAY DIFFRACTION3BB1 - 531 - 53
4X-RAY DIFFRACTION4BB67 - 25467 - 254

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