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- PDB-3amt: Crystal structure of the TiaS-tRNA(Ile2)-ATP complex -

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Basic information

Entry
Database: PDB / ID: 3amt
TitleCrystal structure of the TiaS-tRNA(Ile2)-ATP complex
Components
  • Putative uncharacterized protein
  • RNA (78-MER)
KeywordsRNA BINDING PROTEIN/RNA / TiaS / tRNA(Ile2) / modification / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


tRNAIle2-agmatinylcytidine synthase / ligase activity, forming carbon-nitrogen bonds / tRNA wobble cytosine modification / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
Domain of unknown function DUF1743 / tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS / : / : / : / TiaS FLD domain / TiaS TCKD domain / TiaS C-terminal zinc ribbon domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsNumata, T. / Osawa, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural basis of tRNA agmatinylation essential for AUA codon decoding
Authors: Osawa, T. / Kimura, S. / Terasaka, N. / Inanaga, H. / Suzuki, T. / Numata, T.
History
DepositionAug 23, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: RNA (78-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7373
Polymers76,2302
Non-polymers5071
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-17 kcal/mol
Surface area30120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.105, 131.105, 86.624
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative uncharacterized protein / TiaS


Mass: 51106.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_2259 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O28025
#2: RNA chain RNA (78-MER)


Mass: 25122.984 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: in vitro transcription using T7 RNA polymerase, sequence naturally exist in Archaeoglobus fulgidus
Source: (synth.) Archaeoglobus fulgidus (archaea)
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.37 % / Description: SF file contains friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.085M Tris-HCl pH8.5, 0.17M sodium acetate, 28% PEG 4000, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97898 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 1, 2009 / Details: mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 36616 / % possible obs: 99.9 % / Redundancy: 15.4 % / Biso Wilson estimate: 75.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 29.3
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→47.48 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 60190.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: 1. SF file contains Friedel pairs 2. BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1844 5 %RANDOM
Rwork0.24 ---
obs0.24 36616 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.3582 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 71.4 Å2
Baniso -1Baniso -2Baniso -3
1-9.19 Å20 Å20 Å2
2--9.19 Å20 Å2
3----18.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a1.02 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 2.9→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 1665 31 0 5044
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.54
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.427 321 5.5 %
Rwork0.37 5555 -
obs--95.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramCprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramCdna-rna.top
X-RAY DIFFRACTION3atp_par_2.txtatp.top
X-RAY DIFFRACTION4TPO-100907.paramTPO-100907.top

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