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- PDB-2zuf: Crystal structure of Pyrococcus horikoshii arginyl-tRNA synthetas... -

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Basic information

Entry
Database: PDB / ID: 2zuf
TitleCrystal structure of Pyrococcus horikoshii arginyl-tRNA synthetase complexed with tRNA(Arg)
Components
  • Arginyl-tRNA synthetase
  • tRNA-Arg
KeywordsLigase/RNA / RRS/tRNA(Arg) / Aminoacyl-tRNA synthetase / ATP-binding / Cytoplasm / Ligase / Nucleotide-binding / Protein biosynthesis / Ligase-RNA COMPLEX
Function / homology
Function and homology information


arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Arginyl tRNA synthetase N-terminal domain / Arginine-tRNA ligase / Arginyl tRNA synthetase N-terminal domain / Arginyl-tRNA synthetase, catalytic core domain / Arginyl tRNA synthetase N-terminal domain superfamily / tRNA synthetases class I (R), catalytic domain / Arginyl tRNA synthetase N terminal domain / DALR anticodon binding domain / Arginyl tRNA synthetase N terminal dom / DALR anticodon binding ...Arginyl tRNA synthetase N-terminal domain / Arginine-tRNA ligase / Arginyl tRNA synthetase N-terminal domain / Arginyl-tRNA synthetase, catalytic core domain / Arginyl tRNA synthetase N-terminal domain superfamily / tRNA synthetases class I (R), catalytic domain / Arginyl tRNA synthetase N terminal domain / DALR anticodon binding domain / Arginyl tRNA synthetase N terminal dom / DALR anticodon binding / DALR anticodon binding domain / Isoleucyl-tRNA Synthetase; Domain 1 / Isoleucyl-tRNA Synthetase; Domain 1 / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Gyrase A; domain 2 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Arginine--tRNA ligase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsKonno, M. / Sumida, T. / Uchikawa, E. / Mori, Y. / Yanagisawa, T. / Sekine, S. / Yokoyama, S.
CitationJournal: Febs J. / Year: 2009
Title: Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP)
Authors: Konno, M. / Sumida, T. / Uchikawa, E. / Mori, Y. / Yanagisawa, T. / Sekine, S. / Yokoyama, S.
History
DepositionOct 16, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 21, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / ndb_struct_conf_na ...database_2 / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_assembly_prop.biol_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Apr 30, 2025Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginyl-tRNA synthetase
B: tRNA-Arg


Theoretical massNumber of molelcules
Total (without water)97,6062
Polymers97,6062
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-21 kcal/mol
Surface area37750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.21, 60.14, 110.33
Angle α, β, γ (deg.)90, 107.06, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Arginyl-tRNA synthetase / Arginine--tRNA ligase / ArgRS


Mass: 72444.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: argS, PH1478 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O59147, arginine-tRNA ligase
#2: RNA chain tRNA-Arg


Mass: 25161.041 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This tRNA occurs from Pyrococcus horikoshii, in vitro transcription
Source: (synth.) synthetic construct (others) / References: GenBank: 14589963
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG 4000, 0.2M ammonium sulfate, 5mM magnesium chloride, 100mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2ammonium sulfate11
3magnesium chloride11
4Tris-HCl11
5H2O11
6PEG 400012
7ammonium sulfate12
8magnesium chloride12
9Tris-HCl12
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 24, 2004
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 42799 / Num. obs: 38821 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.2
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.5 / % possible all: 79.4

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2ZUE

2zue


Resolution: 2.3→39.65 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 3892 -RANDOM
Rwork0.2014 ---
obs0.2032 38820 90.7 %-
all-42780 --
Displacement parametersBiso mean: 32.44 Å2
Baniso -1Baniso -2Baniso -3
1-5.314 Å20 Å2-2.109 Å2
2---4.107 Å20 Å2
3----1.207 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5097 1649 0 248 6994
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d1.15
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.3-2.380.35313510.2747X-RAY DIFFRACTION335579.3
2.38-2.480.29963420.2412X-RAY DIFFRACTION347181.7
2.48-2.590.29723610.2342X-RAY DIFFRACTION356684
2.59-2.730.28393860.2272X-RAY DIFFRACTION367186.3
2.73-2.90.29744070.2234X-RAY DIFFRACTION386591.2
2.9-3.120.29023920.2151X-RAY DIFFRACTION398893.5

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