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- PDB-5cm2: Structure of Y. lipolytica Trm9-Trm112 complex, a methyltransfera... -

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Basic information

Entry
Database: PDB / ID: 5cm2
TitleStructure of Y. lipolytica Trm9-Trm112 complex, a methyltransferase modifying U34 in the anticodon loop of some tRNAs
Components
  • TRNA METHYLTRANSFERASE
  • TRNA METHYLTRANSFERASE ACTIVATOR SUBUNIT
KeywordsTRANSFERASE / CLASS I METHYLTRANSFERASE / TRNA METHYLTRANSFERASE / METHYLATION
Function / homology
Function and homology information


tRNA (uridine) methyltransferase activity / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA wobble uridine modification / tRNA methylation / tRNA binding / protein heterodimerization activity / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Probable tRNA methyltransferase 9-like protein / Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein / Methyltransferase type 11 / Methyltransferase domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Single Sheet / Vaccinia Virus protein VP39 ...Probable tRNA methyltransferase 9-like protein / Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein / Methyltransferase type 11 / Methyltransferase domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Single Sheet / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
YALI0E24761p / YALI0D12837p
Similarity search - Component
Biological speciesYarrowia lipolytica CLIB122 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsLetoquart, J. / van Tran, N. / Caroline, V. / Aleksandrov, A. / Lazar, N. / Van Tilbeurgh, H. / Liger, D. / Graille, M.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure.
Authors: Letoquart, J. / van Tran, N. / Caroline, V. / Aleksandrov, A. / Lazar, N. / van Tilbeurgh, H. / Liger, D. / Graille, M.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Mar 17, 2021Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Z: TRNA METHYLTRANSFERASE
M: TRNA METHYLTRANSFERASE ACTIVATOR SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2703
Polymers38,2042
Non-polymers651
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-10 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.200, 176.200, 176.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein TRNA METHYLTRANSFERASE


Mass: 23787.746 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 38-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica CLIB122 (yeast) / Gene: YALI0_D12837g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6C999
#2: Protein TRNA METHYLTRANSFERASE ACTIVATOR SUBUNIT


Mass: 14416.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica CLIB122 (yeast) / Gene: YALI0_E24761g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6C4P5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100MM TRI-SODIUM CITRATE, 20% POLYETHYLENE GLYCOL 4000 (PEG4K), 20% 2-PROPANOL, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
PH range: 7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 110.9801
SYNCHROTRONSOLEIL PROXIMA 121.2819, 1.2826, 1.2753
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELMay 11, 2012
PSI PILATUS 6M2PIXELMay 11, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTALSINGLE WAVELENGTHMx-ray1
2CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTALMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.980111
21.28191
31.28261
41.27531
50.98011
ReflectionResolution: 2.494→50 Å / Num. obs: 16239 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.85 % / Biso Wilson estimate: 52.14 Å2 / Rsym value: 0.069 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 4.85 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.501 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→44.05 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.242 812 5 %Random selection
Rwork0.199 ---
obs0.201 16234 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 1 76 2539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092517
X-RAY DIFFRACTIONf_angle_d1.1933409
X-RAY DIFFRACTIONf_dihedral_angle_d15.355925
X-RAY DIFFRACTIONf_chiral_restr0.05369
X-RAY DIFFRACTIONf_plane_restr0.005445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4943-2.65060.30051320.24392520X-RAY DIFFRACTION98
2.6506-2.85520.3171350.24672557X-RAY DIFFRACTION100
2.8552-3.14250.27191360.24222589X-RAY DIFFRACTION100
3.1425-3.5970.2721360.2242579X-RAY DIFFRACTION99
3.597-4.53110.24071350.1822560X-RAY DIFFRACTION97

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