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- PDB-4q2x: Crystal structure of Arginyl-tRNA synthetase complexed with L-can... -

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Basic information

Entry
Database: PDB / ID: 4q2x
TitleCrystal structure of Arginyl-tRNA synthetase complexed with L-canavanine
ComponentsArginine--tRNA ligase, cytoplasmic
KeywordsLIGASE / HIGH region / Aminoacyl-tRNA synthetase / ATP binding / Arginine binding / tRNA binding
Function / homology
Function and homology information


arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / arginine binding / tRNA binding / cadherin binding ...arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / arginine binding / tRNA binding / cadherin binding / nucleolus / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
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) / Arginyl tRNA synthetase N terminal domain / DALR anticodon binding domain / Arginyl tRNA synthetase N terminal dom / DALR anticodon binding / DALR anticodon binding 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) / Arginyl tRNA synthetase N terminal domain / DALR anticodon binding domain / Arginyl tRNA synthetase N terminal dom / DALR anticodon binding / DALR anticodon binding domain / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
L-CANAVANINE / Arginine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.798 Å
AuthorsKim, H.S. / Jo, C.H. / Cha, S.Y. / Han, A.R. / Hwang, K.Y.
CitationJournal: Febs Lett. / Year: 2014
Title: The crystal structure of arginyl-tRNA synthetase from Homo sapiens
Authors: Kim, H.S. / Cha, S.Y. / Jo, C.H. / Han, A.R. / Hwang, K.Y.
History
DepositionApr 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Arginine--tRNA ligase, cytoplasmic
B: Arginine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,0484
Polymers138,6952
Non-polymers3522
Water3,693205
1
A: Arginine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5242
Polymers69,3481
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arginine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5242
Polymers69,3481
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.393, 109.310, 175.011
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A
21CHAIN B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: -1 - 588 / Label seq-ID: 18 - 607

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1CHAIN AAA
2CHAIN BBB

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Components

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


Mass: 69347.727 Da / Num. of mol.: 2 / Mutation: H438R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RARS / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P54136, arginine-tRNA ligase
#2: Chemical ChemComp-GGB / L-CANAVANINE / L-2-AMINO-4-(GUANIDINOOXY)BUTYRIC ACID / Canavanine


Type: L-peptide linking / Mass: 176.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12N4O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS ISOFORM MONOMERIC, P54136-2.

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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: 2.6 Å3/Da / Density % sol: 52.69 % / Mosaicity: 0.652 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.085mM Sodium citrate tribasic dehydrate, 24% Polyethylene glycol 4000, 0.17M Ammonium acetate, 15% Glycerol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98703 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.98703 Å / Relative weight: 1
ReflectionResolution: 2.798→30 Å / Num. obs: 35623 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 50.99 Å2 / Rmerge(I) obs: 0.103 / Χ2: 2.19 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.853.40.31317010.93995.7
2.85-2.93.60.32517390.97296
2.9-2.963.60.29217311.00396.5
2.96-3.023.80.29317251.0796
3.02-3.083.90.28217201.13996.9
3.08-3.153.90.27317571.21897.3
3.15-3.234.30.22717351.37897
3.23-3.324.50.22617681.41798.1
3.32-3.424.80.20217711.57898.3
3.42-3.5350.18117551.72197.9
3.53-3.655.50.15517842.00298.4
3.65-3.85.70.1417882.21499
3.8-3.975.90.1317952.43998.7
3.97-4.186.30.1217852.81498.9
4.18-4.446.50.10318172.94799
4.44-4.786.80.09518053.07599
4.78-5.266.90.08318112.58798.9
5.26-6.026.70.07918312.24398.7
6.02-7.567.40.06918722.34199
7.56-307.90.06419333.53697.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.798→29.476 Å / FOM work R set: 0.7412 / SU ML: 0.44 / σ(F): 1.51 / Phase error: 31.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2652 1778 5.01 %
Rwork0.2117 --
obs0.2144 35513 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.67 Å2 / Biso mean: 41.72 Å2 / Biso min: 12.01 Å2
Refinement stepCycle: LAST / Resolution: 2.798→29.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9349 0 24 205 9578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019541
X-RAY DIFFRACTIONf_angle_d1.18612845
X-RAY DIFFRACTIONf_chiral_restr0.0491429
X-RAY DIFFRACTIONf_plane_restr0.0061645
X-RAY DIFFRACTIONf_dihedral_angle_d14.8043601
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5582X-RAY DIFFRACTION7.721TORSIONAL
12B5582X-RAY DIFFRACTION7.721TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7977-2.87320.42461410.36782416255792
2.8732-2.95770.3621080.34372541264996
2.9577-3.05310.38211200.3142540266097
3.0531-3.16210.34781530.28822529268297
3.1621-3.28850.31511140.25492581269597
3.2885-3.4380.27711540.24392571272598
3.438-3.61890.27851370.21832571270898
3.6189-3.84520.25111260.19452616274299
3.8452-4.14140.25831470.18762635278299
4.1414-4.55680.24881230.16172655277899
4.5568-5.2130.22021490.15312640278999
5.213-6.55590.26121500.20362675282599
6.5559-29.47730.19181560.16272765292197

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