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- PDB-5gra: Crystal structure of TrmJ from Z. mobilis ZM4 -

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Basic information

Entry
Database: PDB / ID: 5gra
TitleCrystal structure of TrmJ from Z. mobilis ZM4
ComponentstRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
KeywordsTRANSFERASE / methyltransferase / tRNA / TrmJ
Function / homology
Function and homology information


tRNA (cytidine32/uridine32-2'-O)-methyltransferase / tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase activity / tRNA nucleoside ribose methylation / RNA binding / cytosol
Similarity search - Function
RNA methyltransferase TrmJ/LasT / 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/uridine-2'-O-)-methyltransferase TrmJ
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.005 Å
AuthorsGu, D.-H. / Kim, J.-S.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: An asymmetric dimeric structure of TrmJ tRNA methyltransferase from Zymomonas mobilis with a flexible C-terminal dimer
Authors: Gu, D.-H. / Park, M.-Y. / Kim, J.-S.
History
DepositionAug 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
B: tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ


Theoretical massNumber of molelcules
Total (without water)52,9332
Polymers52,9332
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-22 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.232, 41.811, 72.633
Angle α, β, γ (deg.)90.00, 91.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-326-

HOH

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Components

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


Mass: 26466.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: trmJ, ZMO1203 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5NN83, tRNA (cytidine32/uridine32-2'-O)-methyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulfate, MES, Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97952 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 19496 / % possible obs: 97.7 % / Redundancy: 1.8 % / Net I/σ(I): 4.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.005→40.656 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.58
RfactorNum. reflection% reflection
Rfree0.269 535 5.02 %
Rwork0.2322 --
obs0.2341 10647 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.005→40.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3415 0 0 138 3553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033485
X-RAY DIFFRACTIONf_angle_d0.8164749
X-RAY DIFFRACTIONf_dihedral_angle_d17.4552141
X-RAY DIFFRACTIONf_chiral_restr0.044552
X-RAY DIFFRACTIONf_plane_restr0.007624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0054-3.30770.3241290.27832429X-RAY DIFFRACTION97
3.3077-3.7860.30011330.24292525X-RAY DIFFRACTION100
3.786-4.76880.2251340.20592532X-RAY DIFFRACTION100
4.7688-40.65970.26351390.22792626X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 43.5687 Å / Origin y: -22.5466 Å / Origin z: 52.58 Å
111213212223313233
T0.2701 Å2-0.0084 Å2-0.0343 Å2-0.2494 Å2-0.0079 Å2--0.321 Å2
L2.9004 °2-0.2722 °2-0.6363 °2-0.6825 °20.1721 °2--0.9543 °2
S-0.0052 Å °-0.1961 Å °0.0548 Å °0.1256 Å °0.0205 Å °0.0166 Å °-0.0054 Å °-0.1064 Å °-0.0058 Å °
Refinement TLS groupSelection details: all

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