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- PDB-4q2t: Crystal structure of Arginyl-tRNA synthetase complexed with L-arginine -

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Basic information

Entry
Database: PDB / ID: 4q2t
TitleCrystal structure of Arginyl-tRNA synthetase complexed with L-arginine
ComponentsArginine--tRNA ligase, cytoplasmic
KeywordsLIGASE / HIGH region / arginine-tRNA ligase activity / 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 / Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA 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 / Transcriptional and post-translational regulation of MITF-M expression and activity / tRNA binding / cadherin binding / nucleolus / extracellular exosome / nucleoplasm / ATP binding / nucleus / membrane / 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), 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 ...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 / 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 / Arginine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 9, 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.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 8, 2023Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _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)139,2306
Polymers138,6952
Non-polymers5354
Water4,954275
1
A: Arginine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6153
Polymers69,3481
Non-polymers2672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Arginine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6153
Polymers69,3481
Non-polymers2672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.485, 106.901, 175.248
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-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.085mM Sodium citrate tribasic dehydrate, 24% PEG4000, 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: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 55170 / % possible obs: 97.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 44.33 Å2 / Rmerge(I) obs: 0.075 / Χ2: 2.228 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.443.20.30626381.00495.4
2.44-2.493.40.28526941.07696.5
2.49-2.533.40.27526361.10195.8
2.53-2.593.60.25826941.15995.8
2.59-2.643.70.24126601.296.5
2.64-2.73.80.22127231.22197.4
2.7-2.7740.2127281.31697.1
2.77-2.854.30.17727281.45798.1
2.85-2.934.40.16427301.52497.4
2.93-3.024.60.14227211.64598.3
3.02-3.134.80.1327841.77898.6
3.13-3.265.10.11727572.01398.7
3.26-3.415.40.10227812.29499
3.41-3.585.60.09227882.71899
3.58-3.815.70.08227973.17899.3
3.81-4.15.80.07428123.45298.8
4.1-4.5260.06528133.498.9
4.52-5.1760.05528302.78298.7
5.17-6.516.10.05328852.51999.5
6.51-506.10.05129713.11696.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BS2

1bs2


Resolution: 2.4→38.91 Å / FOM work R set: 0.7766 / SU ML: 0.36 / σ(F): 1.5 / Phase error: 28.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 1971 3.63 %
Rwork0.1958 --
obs0.1981 54302 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.63 Å2 / Biso mean: 47.37 Å2 / Biso min: 21.57 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9454 0 36 275 9765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099663
X-RAY DIFFRACTIONf_angle_d1.12213014
X-RAY DIFFRACTIONf_chiral_restr0.0481443
X-RAY DIFFRACTIONf_plane_restr0.0051671
X-RAY DIFFRACTIONf_dihedral_angle_d13.9623662
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5848X-RAY DIFFRACTION6.214TORSIONAL
12B5848X-RAY DIFFRACTION6.214TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.460.35681360.32423603373996
2.46-2.52650.34431350.29753595373096
2.5265-2.60080.32131370.27853640377796
2.6008-2.68480.36591380.25553655379397
2.6848-2.78070.28311400.23783686382697
2.7807-2.8920.28331390.21993709384898
2.892-3.02360.27271380.21343701383998
3.0236-3.18290.26311410.2253738387999
3.1829-3.38220.29551430.21213770391399
3.3822-3.64320.25131410.19953769391099
3.6432-4.00950.27131430.1863794393799
4.0095-4.58890.22551440.15953819396399
4.5889-5.77850.24041460.16033872401899
5.7785-38.9150.19431500.15583980413098

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