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- PDB-4jak: Crystal structure of tRNA (Um34/Cm34) methyltransferase TrmL from... -

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Basic information

Entry
Database: PDB / ID: 4jak
TitleCrystal structure of tRNA (Um34/Cm34) methyltransferase TrmL from Escherichia coli
ComponentstRNA (cytidine(34)-2'-O)-methyltransferase
KeywordsTRANSFERASE / SPOUT / tRNA modification / methyltransferase / deep trefoil knot / SAM binding / methylation
Function / homology
Function and homology information


wobble position cytosine ribose methylation / wobble position uridine ribose methylation / tRNA (cytidine(34)-2'-O)-methyltransferase activity / tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity / tRNA (cytidine34-2'-O)-methyltransferase / protein homodimerization activity / RNA binding / cytoplasm
Similarity search - Function
tRNA (cytidine/uridine-2'-O-)-methyltransferase / tRNA/rRNA methyltransferase, SpoU type / SpoU rRNA Methylase family / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA (cytidine(34)-2'-O)-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, R.J. / Zhou, M. / Wang, E.D.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL
Authors: Liu, R.J. / Zhou, M. / Fang, Z.P. / Wang, M. / Zhou, X.L. / Wang, E.D.
History
DepositionFeb 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA (cytidine(34)-2'-O)-methyltransferase
B: tRNA (cytidine(34)-2'-O)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)37,6652
Polymers37,6652
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-7 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.949, 84.949, 78.895
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein tRNA (cytidine(34)-2'-O)-methyltransferase / tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL


Mass: 18832.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: trmL, yibK, b3606, JW3581 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AGJ7, tRNA (cytidine34-2'-O)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 4.36 Å3/Da / Density % sol: 71.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% polyethylene glycol (PEG) 3350, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 43047 / Num. obs: 42546 / % possible obs: 98.8 %
Reflection shellResolution: 2→2.07 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J85

1j85


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20351 2140 5 %RANDOM
Rwork0.18934 ---
obs0.19004 40388 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.285 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 0 214 2664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222516
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.9593426
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7725308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51322.667120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94815392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1941524
X-RAY DIFFRACTIONr_chiral_restr0.0840.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211968
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_it4.3851.51552
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.86722502
X-RAY DIFFRACTIONr_scbond_it6.6863964
X-RAY DIFFRACTIONr_scangle_it8.4364.5924
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 146 -
Rwork0.273 2868 -
obs--94.87 %

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