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- PDB-1jii: Crystal structure of S. aureus TyrRS in complex with SB-219383 -

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Basic information

Entry
Database: PDB / ID: 1jii
TitleCrystal structure of S. aureus TyrRS in complex with SB-219383
Componentstyrosyl-tRNA synthetase
KeywordsLIGASE / tyrosyl-trna synthetase / staphylococcus aureus / truncation / structure based inhibitor design
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / RNA binding / ATP binding / cytoplasm
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 / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / 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. ...Tyrosine-tRNA ligase, bacterial-type, type 1 / Tyrosine--tRNA ligase SYY-like C-terminal domain / Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / 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. / HUPs / 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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-383 / : / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsQiu, X. / Janson, C.A. / Smith, W.W. / Jarvest, R.L.
CitationJournal: Protein Sci. / Year: 2001
Title: Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors.
Authors: Qiu, X. / Janson, C.A. / Smith, W.W. / Green, S.M. / McDevitt, P. / Johanson, K. / Carter, P. / Hibbs, M. / Lewis, C. / Chalker, A. / Fosberry, A. / Lalonde, J. / Berge, J. / Brown, P. / ...Authors: Qiu, X. / Janson, C.A. / Smith, W.W. / Green, S.M. / McDevitt, P. / Johanson, K. / Carter, P. / Hibbs, M. / Lewis, C. / Chalker, A. / Fosberry, A. / Lalonde, J. / Berge, J. / Brown, P. / Houge-Frydrych, C.S. / Jarvest, R.L.
History
DepositionJul 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0692
Polymers47,6551
Non-polymers4131
Water00
1
A: tyrosyl-tRNA synthetase
hetero molecules

A: tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1384
Polymers95,3112
Non-polymers8272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
2
A: tyrosyl-tRNA synthetase
hetero molecules

A: tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1384
Polymers95,3112
Non-polymers8272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area4580 Å2
ΔGint-38 kcal/mol
Surface area27850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.560, 98.450, 142.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
Detailsthe biological assembly is a dimer generated from the monomer in ASU and the operation -x,y,-z+1/2 ---- operation 3

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Components

#1: Protein tyrosyl-tRNA synthetase / E.C.6.1.1.1 / TYROSINE--TRNA LIGASE / TYRRS / Tyrosyl-Transfer RNA Synthetase


Mass: 47655.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Variant: aureus N315 / Production host: Escherichia coli (E. coli)
References: GenBank: 13701524, UniProt: A6QHR2*PLUS, tyrosine-tRNA ligase
#2: Chemical ChemComp-383 / [2-AMINO-3-(4-HYDROXY-PHENYL)-PROPIONYLAMINO]- (2,4,5,8-TETRAHYDROXY-7-OXA-2-AZA-BICYCLO[3.2.1]OCT-3-YL)- ACETIC ACID / SB-219383


Mass: 413.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N3O9

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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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: PEG 1000, CaCl2, pH 7.25, VAPOR DIFFUSION, SITTING DROP at 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
212-15 MPEG10001reservoir
30.15 M1reservoirCaCl2
40.2 Mimidazole1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 6, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→27 Å / Num. all: 8608 / Num. obs: 8530 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 7.9
Reflection shellResolution: 3.2→3.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 1.9 / % possible all: 99
Reflection
*PLUS
% possible obs: 99 % / Num. measured all: 31808
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B. stearothermophilus

Resolution: 3.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.335 350 5 %random
Rwork0.269 ---
obs-7179 --
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 29 0 2585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.9
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.269
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.9

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