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- PDB-4rvz: Crystal structure of tRNA fluorescent labeling enzyme -

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Basic information

Entry
Database: PDB / ID: 4rvz
TitleCrystal structure of tRNA fluorescent labeling enzyme
ComponentstRNA(Ile2) 2-agmatinylcytidine synthetase TiaS
KeywordsLIGASE / tRNA modification / phosphorylation / tias
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 / Domain of unknown function (DUF1743) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / N-(4-aminobutyl)-2-azidoacetamide / tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDong, J. / Li, F. / Wang, J. / Gong, W.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: A covalent approach for site-specific RNA labeling in Mammalian cells.
Authors: Li, F. / Dong, J. / Hu, X. / Gong, W. / Li, J. / Shen, J. / Tian, H. / Wang, J.
History
DepositionNov 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Apr 3, 2024Group: 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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
Z: tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1636
Polymers48,3721
Non-polymers7905
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.623, 69.623, 211.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS / tRNA(Ile2)-agm2C synthetase / tRNA(Ile2) agmatidine synthetase


Mass: 48372.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: tiaS, AF_2259 / Plasmid: pET22b/pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O28025, tRNAIle2-agmatinylcytidine synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZNN / N-(4-aminobutyl)-2-azidoacetamide


Mass: 171.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13N5O

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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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mM HEPES, pH 7.0-7.2, 0.5 M NH4Ac, 0.02 M MgCl2, 1.5-2.5% PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 11960 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.9→3 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 8.6 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MLPHAREphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: selenomethionine derived Tias coordinate

Resolution: 2.9→29.066 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 33.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2919 572 4.82 %
Rwork0.2098 --
obs0.214 11869 96.95 %
all-11960 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→29.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 46 0 3417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083483
X-RAY DIFFRACTIONf_angle_d1.2634710
X-RAY DIFFRACTIONf_dihedral_angle_d16.8521331
X-RAY DIFFRACTIONf_chiral_restr0.085513
X-RAY DIFFRACTIONf_plane_restr0.005611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.18860.36431310.23432812X-RAY DIFFRACTION99
3.1886-3.64920.35181400.2382842X-RAY DIFFRACTION99
3.6492-4.59470.31511470.20822832X-RAY DIFFRACTION98
4.5947-29.06760.25251540.19642811X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 22.6892 Å / Origin y: 7.9868 Å / Origin z: 51.0628 Å
111213212223313233
T0.6286 Å20.0942 Å20.0633 Å2-0.5256 Å20.038 Å2--0.5687 Å2
L2.1374 °2-0.2251 °21.6922 °2-0.5655 °2-0.0251 °2--2.7104 °2
S-0.1002 Å °-0.1939 Å °-0.0079 Å °-0.0533 Å °0.0865 Å °-0.0602 Å °-0.4051 Å °0.0773 Å °0.0271 Å °
Refinement TLS groupSelection details: ( CHAIN Z AND RESID 1:420 )

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