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- PDB-7ap3: Crystal structure of E. coli tyrosyl-tRNA synthetase in complex w... -

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Basic information

Entry
Database: PDB / ID: 7ap3
TitleCrystal structure of E. coli tyrosyl-tRNA synthetase in complex with TyrS7HMDDA
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / protein-inhibitor complex / tRNA aminoacylation
Function / homology
Function and homology information


tRNA aminoacylation / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / protein homodimerization activity / RNA binding / ATP binding / membrane / cytosol
Similarity search - Function
: / Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine--tRNA ligase SYY-like C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold ...: / Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine--tRNA ligase SYY-like C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily
Similarity search - Domain/homology
Chem-RRB / Tyrosine--tRNA ligase / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDe Graef, S. / Pang, L. / Strelkov, S.V. / Weeks, S.D.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S53518N Belgium
CitationJournal: Molecules / Year: 2020
Title: Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors.
Authors: Zhang, B. / Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Lescrinier, E. / Rozenski, J. / Strelkov, S.V. / Weeks, S.D. / Van Aerschot, A.
History
DepositionOct 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Tyrosine--tRNA ligase
B: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3116
Polymers95,1902
Non-polymers1,1214
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-46 kcal/mol
Surface area35800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.166, 65.124, 90.978
Angle α, β, γ (deg.)90.000, 101.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine--tRNA ligase / Tyrosyl-tRNA synthetase / TyrRS


Mass: 47594.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Strain: DE3 / Gene: tyrS, ECBD_2006 / Plasmid: pETRUK / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: A0A140NBN7, UniProt: P0AGJ9*PLUS, tyrosine-tRNA ligase
#2: Chemical ChemComp-RRB / [(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate


Mass: 537.543 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H27N5O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: Holo enzyme crystals were grown in 0.1 M BIS-TRIS pH 6.5, 10-15% PEG 3350, 20 mM glutamate pH 6 (1M stock solution adjusted to pH 5) and 20% (v/v) ethylene glycol. For soaking crystals were ...Details: Holo enzyme crystals were grown in 0.1 M BIS-TRIS pH 6.5, 10-15% PEG 3350, 20 mM glutamate pH 6 (1M stock solution adjusted to pH 5) and 20% (v/v) ethylene glycol. For soaking crystals were transferred to a drop containing mother liquor supplemented with 2 mM inhibitor.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.968625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968625 Å / Relative weight: 1
ReflectionResolution: 1.998→65.12 Å / Num. obs: 63743 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 29.52 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.065 / Rrim(I) all: 0.126 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.110.9063275992660.7110.5571.0671.499.5
6.32-65.120.035739121220.9990.0210.04122.499.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUD

4oud


Resolution: 2→54.681 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 2467 3.88 %
Rwork0.2028 61154 -
obs0.2048 63621 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.77 Å2 / Biso mean: 41.4637 Å2 / Biso min: 16.55 Å2
Refinement stepCycle: final / Resolution: 2→54.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6428 0 76 481 6985
Biso mean--30.72 41.2 -
Num. residues----826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076635
X-RAY DIFFRACTIONf_angle_d0.8448988
X-RAY DIFFRACTIONf_chiral_restr0.048985
X-RAY DIFFRACTIONf_plane_restr0.0051219
X-RAY DIFFRACTIONf_dihedral_angle_d7.23958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.03630.32011510.3086339599
2.0363-2.07790.36131180.2952335199
2.0779-2.12310.33691460.28336799
2.1231-2.17250.32981380.2677339999
2.1725-2.22680.28581370.2464338199
2.2268-2.2870.31351410.2493335899
2.287-2.35430.28621270.2389339099
2.3543-2.43030.28581320.22793405100
2.4303-2.51720.29721350.22293392100
2.5172-2.61790.28141430.2119339299
2.6179-2.73710.321520.2108338499
2.7371-2.88140.27311260.2112337999
2.8814-3.06190.25431450.208340699
3.0619-3.29830.221340.2001339699
3.2983-3.63010.22421380.1899342799
3.6301-4.15530.20171170.165341999
4.1553-5.23460.19261570.1605338198
5.2346-54.6810.25661300.1795353299
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)
11.3807-0.21591.41261.1021-0.44582.3963-0.0507-0.22310.02960.11320.00410.0027-0.1087-0.20620.03080.22690.0119-0.01070.322-0.0170.1884-39.04062.1689-9.5796
22.7052-1.7219-1.83283.64151.6633.01420.0059-0.09430.11390.1933-0.0049-0.3119-0.19150.28530.01310.3389-0.0499-0.08990.36410.03610.2369-17.20467.57257.9976
32.7571.7023-0.34861.0565-0.23240.07010.28230.0263-0.0589-1.0389-0.0304-1.883-0.08420.44170.0740.468-0.00830.49250.73410.00531.44839.31194.6147-3.2653
42.00280.21110.57850.9365-0.00041.9513-0.02360.17170.0368-0.06250.0310.0167-0.02140.0432-0.00920.19460.0022-0.02870.20990.0070.2279-48.75140.9213-45.1946
52.83671.53520.07860.9403-0.21290.6741-0.09340.36080.6821-0.01430.09820.3018-0.0956-0.14850.00220.22570.0187-0.04650.31750.040.3351-64.03457.9659-54.2067
63.4119-0.1449-0.22370.4853-0.00060.68620.04030.41820.1019-0.0013-0.0616-0.0264-0.04330.1708-0.0090.2072-0.0166-0.03180.29870.0490.2057-86.95294.8879-58.2371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 235 )A5 - 235
2X-RAY DIFFRACTION2chain 'A' and (resid 243 through 329 )A243 - 329
3X-RAY DIFFRACTION3chain 'A' and (resid 330 through 424 )A330 - 424
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 216 )B5 - 216
5X-RAY DIFFRACTION5chain 'B' and (resid 217 through 267 )B217 - 267
6X-RAY DIFFRACTION6chain 'B' and (resid 268 through 424 )B268 - 424

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