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- PDB-3tma: Crystal structure of TrmN from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 3tma
TitleCrystal structure of TrmN from Thermus thermophilus
Componentsmethyltransferase
KeywordsTRANSFERASE / Rossmann fold methyltransferase / THUMP domain / tRNA methyltransferase
Function / homology
Function and homology information


tRNA (guanine6-N2)-methyltransferase / tRNA processing / methyltransferase activity / methylation / RNA binding / cytoplasm
Similarity search - Function
VC0802-like - #30 / Ribosomal RNA large subunit methyltransferase K/L-like, FLD domain / RMKL-like, methyltransferase domain / THUMP / THUMP domain / THUMP domain / THUMP domain profile. / VC0802-like / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...VC0802-like - #30 / Ribosomal RNA large subunit methyltransferase K/L-like, FLD domain / RMKL-like, methyltransferase domain / THUMP / THUMP domain / THUMP domain / THUMP domain profile. / VC0802-like / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / tRNA (guanine(6)-N2)-methyltransferase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsFislage, M. / Roovers, M. / Tuszynska, I. / Bujnicki, J.M. / Droogmans, L. / Versees, W.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life.
Authors: Fislage, M. / Roovers, M. / Tuszynska, I. / Bujnicki, J.M. / Droogmans, L. / Versees, W.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Other
Revision 1.2Oct 3, 2012Group: Database references
Revision 1.3Sep 13, 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 / pdbx_struct_special_symmetry / 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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1732
Polymers39,0781
Non-polymers951
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: methyltransferase
hetero molecules

A: methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3464
Polymers78,1562
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area1910 Å2
ΔGint-19 kcal/mol
Surface area29820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.860, 65.860, 144.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-673-

HOH

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Components

#1: Protein methyltransferase


Mass: 39078.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TTC1157, TT_C1157 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q72IH5, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 100 mM citrate/phosphate, 15% PEG 6000, 200 mM NaCl, 100 mM sodium citrate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 27, 2010
RadiationMonochromator: monochromator (horizontally side diffracting Silicon 111 crystal)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 23538 / Num. obs: 23534 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 22.4
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 22.1 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 7.37 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TLJ

3tlj


Resolution: 2.05→44.77 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.886 / SU ML: 0.098 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21176 1177 5 %RANDOM
Rwork0.15423 ---
obs0.15707 22355 100 %-
all-23534 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.969 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.05→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2595 0 5 196 2796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9953699
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7535348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.36220.25120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28915445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9921541
X-RAY DIFFRACTIONr_chiral_restr0.1320.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0222102
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4551.51682
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.47722690
X-RAY DIFFRACTIONr_scbond_it3.84131033
X-RAY DIFFRACTIONr_scangle_it6.0924.51000
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 85 -
Rwork0.178 1617 -
obs--100 %
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)
11.4655-0.5160.53211.1338-0.1931.5339-0.0688-0.03720.00050.06160.0868-0.105-0.00960.0498-0.01790.0824-0.01490.01210.0905-0.01660.015413.2632.98855.408
22.7720.4161.87650.18170.47091.57660.03380.2555-0.06980.03570.0348-0.0410.06040.1502-0.06860.1534-0.00040.00830.17750.01020.09243.64628.30846.109
31.82780.4252-0.36921.0698-0.68953.6175-0.06780.131-0.1075-0.10960.0856-0.03460.329-0.0326-0.01770.0448-0.02980.00180.1026-0.03320.0179-11.722.43228.168
44.9408-0.40071.07630.90180.49992.1619-0.15060.1252-0.0805-0.05190.14540.0453-0.08480.10350.00520.0752-0.02570.01290.12970.02810.0472-0.39833.54124.057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 133
2X-RAY DIFFRACTION2A134 - 183
3X-RAY DIFFRACTION3A184 - 296
4X-RAY DIFFRACTION4A297 - 335

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