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- PDB-2j5b: Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyph... -

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Basic information

Entry
Database: PDB / ID: 2j5b
TitleStructure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynol
ComponentsTYROSYL-TRNA SYNTHETASE
KeywordsLIGASE / PROTEIN BIOSYNTHESIS / ATP-BINDING
Function / homology
Function and homology information


L-tyrosine binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / protein homodimerization activity / ATP binding / identical protein binding
Similarity search - Function
Tyrosine-tRNA ligase, archaeal/eukaryotic-type / : / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle ...Tyrosine-tRNA ligase, archaeal/eukaryotic-type / : / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-[(2S)-2-amino-3-hydroxypropyl]phenol / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesACANTHAMOEBA POLYPHAGA MIMIVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAbergel, C. / Rudinger-thirion, J. / Giege, R. / Claverie, J.M.
Citation
Journal: J.Virol. / Year: 2007
Title: Virus-Encoded Aminoacyl-tRNA Synthetases: Structural and Functional Characterization of Mimivirus Tyrrs and Metrs.
Authors: Abergel, C. / Rudinger-Thirion, J. / Giege, R. / Claverie, J.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Mimivirus Tyrrs: Preliminary Structural and Functional Characterization of the First Amino- Acyl tRNA Synthetase Found in a Virus.
Authors: Abergel, C. / Chenivesse, S. / Byrne, D. / Suhre, K. / Arondel, V. / Claverie, J.-M.
History
DepositionSep 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 17, 2018Group: Data collection / Structure summary / Category: chem_comp
Item: _chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms / _chem_comp.type
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: TYROSYL-TRNA SYNTHETASE
B: TYROSYL-TRNA SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1264
Polymers79,7912
Non-polymers3342
Water5,945330
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-21.1 kcal/mol
Surface area29100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.502, 107.300, 148.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.10962, -0.99355, -0.02886), (-0.99394, 0.1098, -0.00465), (0.00779, 0.02817, -0.99957)
Vector: 106.36381, 94.10122, 57.46155)

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Components

#1: Protein TYROSYL-TRNA SYNTHETASE / TYROSINE-TRNA LIGASE / TYRRS / TYROSYL-TRNA SYNTHETASE


Mass: 39895.703 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACANTHAMOEBA POLYPHAGA MIMIVIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q5UPJ7, tyrosine-tRNA ligase
#2: Chemical ChemComp-TYE / 4-[(2S)-2-amino-3-hydroxypropyl]phenol / tyrosinol / bound form of TYROSINAL


Type: L-peptide linking / Mass: 167.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN TERMINAL EXTENSION DUE TO GATEWAY CLONING

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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: 3.17 Å3/Da / Density % sol: 61.18 %
Description: STRUCTURE WAS SOLVED USING TYRRS WITH SELENO SUBSTITUTED METHIONINE AND INCOMPLETE MAD DATASET AT 3.5 AMGSTROM RESOLUTION. THE UNREFINED CONSTRUCTION WAS USED AS MODEL FOR MOLECULAR ...Description: STRUCTURE WAS SOLVED USING TYRRS WITH SELENO SUBSTITUTED METHIONINE AND INCOMPLETE MAD DATASET AT 3.5 AMGSTROM RESOLUTION. THE UNREFINED CONSTRUCTION WAS USED AS MODEL FOR MOLECULAR REPLACEMENT WITH THE NATIVE DATASET
Crystal growpH: 5.5
Details: RESERVOIR: 0.1 M SODIUM CITRATE BUFFER PH 5.5, PEG 4000 8% (W/V), 15% MPD (V/V), 0.1M KCL, 1MM MGCL2 DROPLET: 2 MICROL TYRRS 14 MG/ML IN 20 MM TRIS PH 7.4, 1MM TYROSINOL, 1MM ATP 0.5 MICROL RESERVOIR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97925
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 19, 2006 / Details: MIRROR
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.2→87 Å / Num. obs: 52537 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 2.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LOW RESOLUTION MAD STRUCTURE

Resolution: 2.2→29.83 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2137340.15 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CHAIN A WAS NOT MODELED. DISORDERED REGION 142 TO 158 CHAIN B WAS NOT MODELED. DISORDERED REGION 223 TO 226 CHAIN B WAS MODELED USING RESIDUAL DENSITY AND STEREOCHEMISTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2641 5 %RANDOM
Rwork0.216 ---
obs0.216 52432 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.7184 Å2 / ksol: 0.32568 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1--4.07 Å20 Å20 Å2
2--5.05 Å20 Å2
3----0.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5169 0 24 330 5523
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.322
X-RAY DIFFRACTIONc_scbond_it2.382
X-RAY DIFFRACTIONc_scangle_it3.482.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 462 5.4 %
Rwork0.248 8152 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3TYB.PARAMTYB.TOP

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