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- PDB-5yym: Crystal structures of E.coli arginyl-trna synthetase (argrs) in c... -

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Basic information

Entry
Database: PDB / ID: 5yym
TitleCrystal structures of E.coli arginyl-trna synthetase (argrs) in complex with substrate Arg
ComponentsArginine--tRNA ligase
KeywordsLIGASE / BACTERIAL AMINOACYL-TRNA SYNTHETASES / TRNA ARGINYLATION / DEGENERATED CLASS I SIGNATURE SEQUENCES / TRNA(ARG) IDENTITY ELEMENTS / CONFORMATIONAL ADAPTATION
Function / homology
Function and homology information


arginine-tRNA ligase / arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / ATP binding / cytosol
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) / 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) / 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. / Gyrase A; domain 2 / Rossmann-like alpha/beta/alpha sandwich fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ARGININE / Arginine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhou, M. / Ye, S. / Stephen, P. / Zhang, R.G. / Wang, E.D. / Giege, R. / Lin, S.X.
CitationJournal: To Be Published
Title: Crystal Structures Of E.Coli Arginyl-Trna Synthetase (Argrs) In Complex With Substrates
Authors: Zhou, M. / Ye, S. / Stephen, P. / Zhang, R.G. / Wang, E.D. / Giege, R. / Lin, S.X.
History
DepositionDec 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginine--tRNA ligase
B: Arginine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,9024
Polymers131,5522
Non-polymers3502
Water8,773487
1
A: Arginine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9512
Polymers65,7761
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arginine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9512
Polymers65,7761
Non-polymers1751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.727, 244.510, 52.460
Angle α, β, γ (deg.)90.00, 90.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 65775.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: argS, b1876, JW1865 / Production host: Escherichia coli (E. coli) / References: UniProt: P11875, 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 22% PEG8 000, 0.1 M NaH2PO4/Na2HPO4 pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2010
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 57753 / % possible obs: 91.5 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2.9 / % possible all: 88.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BS2

1bs2


Resolution: 2.2→40.75 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.64
RfactorNum. reflection% reflection
Rfree0.251 2903 5.03 %
Rwork0.197 --
obs0.199 57753 91.5 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 2.2→40.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9097 0 24 487 9608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039292
X-RAY DIFFRACTIONf_angle_d0.69812554
X-RAY DIFFRACTIONf_dihedral_angle_d14.4083462
X-RAY DIFFRACTIONf_chiral_restr0.0491385
X-RAY DIFFRACTIONf_plane_restr0.0031640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23610.37481150.25162467X-RAY DIFFRACTION86
2.2361-2.27460.29861380.23452480X-RAY DIFFRACTION87
2.2746-2.3160.26591380.22332423X-RAY DIFFRACTION86
2.316-2.36050.27111110.21582522X-RAY DIFFRACTION87
2.3605-2.40870.25851410.22072467X-RAY DIFFRACTION88
2.4087-2.46110.31221290.21882541X-RAY DIFFRACTION89
2.4611-2.51830.29751560.21582540X-RAY DIFFRACTION89
2.5183-2.58130.25921390.21722565X-RAY DIFFRACTION90
2.5813-2.65110.29091240.22082598X-RAY DIFFRACTION90
2.6511-2.72910.30491340.2212616X-RAY DIFFRACTION92
2.7291-2.81710.26551380.21842585X-RAY DIFFRACTION91
2.8171-2.91780.28771230.20922738X-RAY DIFFRACTION93
2.9178-3.03460.28251200.22072695X-RAY DIFFRACTION95
3.0346-3.17260.28681710.22742710X-RAY DIFFRACTION96
3.1726-3.33980.27941480.20712771X-RAY DIFFRACTION97
3.3398-3.5490.26041370.19552789X-RAY DIFFRACTION97
3.549-3.82280.21111680.17512708X-RAY DIFFRACTION96
3.8228-4.20710.21511490.16662654X-RAY DIFFRACTION94
4.2071-4.81510.2011260.15522686X-RAY DIFFRACTION93
4.8151-6.06330.22891690.18692615X-RAY DIFFRACTION93
6.0633-40.75860.21971290.18272680X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1479-0.02720.93112.7795-0.11341.23620.12950.05930.35330.3392-0.2191-0.7296-0.08880.31410.2020.3439-0.0618-0.05120.33130.08830.418635.562894.332831.0662
20.8675-0.9059-0.11691.74920.61280.98190.08430.12770.0488-0.1543-0.1230.2632-0.1787-0.19640.00630.27060.017-0.00130.2673-0.05210.29440.0536127.420825.2648
31.7187-0.54810.01392.71251.13472.29380.05150.2924-0.1417-1.0271-0.11290.2288-0.25340.0498-0.01470.56160.0249-0.11270.1863-0.05660.25668.655118.603513.8257
41.2063-0.14860.51964.40041.06252.22880.04710.04470.0548-0.2698-0.16110.0929-0.0256-0.0660.09430.2321-0.00470.02140.2176-0.020.121712.893393.666813.3589
52.1241.0334-0.72542.67630.52611.89540.0789-0.1094-0.09930.3657-0.41180.72990.3576-0.54410.29920.4904-0.10730.09750.3837-0.13990.4157-6.521267.290856.8339
62.6664-2.97950.17845.53510.07650.86850.21290.1315-0.0299-0.2262-0.1362-0.1194-0.01420.1896-0.14130.2606-0.04770.00420.19560.00540.189628.307743.032648.3556
71.2745-0.5828-0.27920.7419-0.38291.09680.08310.1003-0.2186-0.1746-0.05430.03740.19460.0407-0.01870.4236-0.0404-0.00430.23620.01870.296325.014930.199152.9009
80.6783-0.6743-0.27283.9449-0.19561.91130.02340.1428-0.0313-0.664-0.1564-0.28320.47450.15750.07360.45780.0340.04620.27360.02140.188821.51260.124532.8153
91.0454-0.5219-0.21745.3431-0.70982.37880.0313-0.00140.0006-0.0321-0.07340.1823-0.0672-0.08920.0660.2153-0.01940.00580.1945-0.03810.116512.992270.328442.4031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID -7:100 )
2X-RAY DIFFRACTION2(CHAIN A AND RESID 101:338 )
3X-RAY DIFFRACTION3(CHAIN A AND RESID 339:413 )
4X-RAY DIFFRACTION4(CHAIN A AND (RESID 414:577 OR RESID 1001:1001 ) )
5X-RAY DIFFRACTION5(CHAIN B AND RESID -6:101 )
6X-RAY DIFFRACTION6(CHAIN B AND RESID 102:191 )
7X-RAY DIFFRACTION7(CHAIN B AND RESID 192:371 )
8X-RAY DIFFRACTION8(CHAIN B AND RESID 372:490 )
9X-RAY DIFFRACTION9(CHAIN B AND (RESID 491:577 OR RESID 1001:1001 ) )

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