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- PDB-4q2y: Crystal structure of Arginyl-tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 4q2y
TitleCrystal structure of Arginyl-tRNA synthetase
ComponentsArginine--tRNA ligase, cytoplasmic
KeywordsLIGASE / HIGH region / arginine-tRNA ligase / ATP binding / tRNA binding / Arginine binding
Function / homology
Function and homology information


arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / Selenoamino acid metabolism / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / arginine binding / tRNA binding / cadherin binding ...arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / Selenoamino acid metabolism / aminoacyl-tRNA synthetase multienzyme complex / Cytosolic tRNA aminoacylation / 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
Arginine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.799 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
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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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


Theoretical massNumber of molelcules
Total (without water)138,6952
Polymers138,6952
Non-polymers00
Water3,081171
1
A: Arginine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)69,3481
Polymers69,3481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arginine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)69,3481
Polymers69,3481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.623, 105.234, 172.259
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 / End auth comp-ID: MET / End label comp-ID: MET

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYCHAIN AAA-10 - 5889 - 607
2ALAALACHAIN BBB-1 - 58818 - 607

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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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.54 Å3/Da / Density % sol: 51.5 % / Mosaicity: 1.014 °
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: Photon Factory / Beamline: BL-1A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.799→50 Å / Num. obs: 33971 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.086 / Χ2: 2.172 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.853.40.31415611.5789.1
2.85-2.93.60.315781.53990.7
2.9-2.963.80.27915901.68290.7
2.96-3.023.90.27116051.69491.9
3.02-3.083.80.26916301.87293.3
3.08-3.154.20.24916181.83693.3
3.15-3.234.40.2221678294.6
3.23-3.324.70.20616692.05695.2
3.32-3.4250.17216832.21695.8
3.42-3.535.20.15117202.20596.6
3.53-3.655.80.12316912.36897.4
3.65-3.85.90.10917302.35498.2
3.8-3.976.30.09417432.37298.4
3.97-4.186.80.08217512.40698.5
4.18-4.4470.06917482.3798.6
4.44-4.797.50.06217882.34198.9
4.79-5.277.70.06117732.30198.9
5.27-6.037.90.06217972.19399
6.03-7.5980.05418132.11499.1
7.59-5080.04618052.24992.2

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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
Starting model: 1BS2

1bs2


Resolution: 2.799→44.901 Å / FOM work R set: 0.7992 / SU ML: 0.46 / σ(F): 1.54 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 1712 5.05 %
Rwork0.2081 --
obs0.2112 33922 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.39 Å2 / Biso mean: 47.3 Å2 / Biso min: 9.64 Å2
Refinement stepCycle: LAST / Resolution: 2.799→44.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9162 0 0 171 9333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019330
X-RAY DIFFRACTIONf_angle_d1.38412563
X-RAY DIFFRACTIONf_chiral_restr0.091396
X-RAY DIFFRACTIONf_plane_restr0.0071607
X-RAY DIFFRACTIONf_dihedral_angle_d15.3253513
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5210X-RAY DIFFRACTION13.729TORSIONAL
12B5210X-RAY DIFFRACTION13.729TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7995-2.88180.38681300.31072451258188
2.8818-2.97480.3521200.27582539265991
2.9748-3.08110.32321230.25892580270393
3.0811-3.20450.32071440.24942583272794
3.2045-3.35030.32061450.23872661280696
3.3503-3.52680.31841570.21562666282396
3.5268-3.74770.23491330.18462731286498
3.7477-4.03690.2351390.17352743288298
4.0369-4.44280.20981570.16472763292099
4.4428-5.08490.22851630.15962804296799
5.0849-6.40350.23871530.21262835298899
6.4035-44.9070.26531480.21352854300295

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