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- PDB-4qbt: Crystal structure of tyrosine bound human tyrosyl tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 4qbt
TitleCrystal structure of tyrosine bound human tyrosyl tRNA synthetase
ComponentsTyrosine--tRNA ligase, cytoplasmic
KeywordsLIGASE / tyrosine / aminoacyl tRNA synthetase / Rossman fold / aminoacid activation / tRNA / ester bond
Function / homology
Function and homology information


interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process ...interleukin-8 receptor binding / tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / Cytosolic tRNA aminoacylation / response to starvation / small molecule binding / tRNA binding / nuclear body / apoptotic process / extracellular space / RNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold ...Tyrosine-tRNA ligase / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Nucleic acid-binding, OB-fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / TYROSINE / Tyrosine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMathew, S. / Schimmel, P.
CitationJournal: Nature / Year: 2014
Title: A human tRNA synthetase is a potent PARP1-activating effector target for resveratrol.
Authors: Sajish, M. / Schimmel, P.
History
DepositionMay 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Mar 25, 2015Group: Database references
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Tyrosine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,95810
Polymers42,1341
Non-polymers8259
Water3,171176
1
A: Tyrosine--tRNA ligase, cytoplasmic
hetero molecules

A: Tyrosine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,91620
Polymers84,2672
Non-polymers1,64918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area5820 Å2
ΔGint-72 kcal/mol
Surface area29370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.251, 162.641, 35.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-759-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 42133.559 Da / Num. of mol.: 1 / Fragment: mini TyrRS (UNP residues 1-364)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YARS / Production host: Escherichia coli (E. coli) / References: UniProt: P54577, tyrosine-tRNA ligase

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Non-polymers , 6 types, 185 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.1 M ammonium sulfate, 0.1 M sodium phosphate monobasic, pH 6-8, 2% acetone, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2012
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→34.63 Å / Num. all: 26174 / Num. obs: 24513 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1285 / Rsym value: 0.441 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q11

1q11


Resolution: 2.1→34.63 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.593 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.214 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1312 5.1 %RANDOM
Rwork0.21311 ---
obs0.21584 24513 97.98 %-
all-26174 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.199 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å20 Å20 Å2
2---1.66 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 47 176 2853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192732
X-RAY DIFFRACTIONr_bond_other_d0.0010.022701
X-RAY DIFFRACTIONr_angle_refined_deg2.0082.0033690
X-RAY DIFFRACTIONr_angle_other_deg0.86836254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5685329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50324.912114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60315508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.524159
X-RAY DIFFRACTIONr_chiral_restr0.1040.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212957
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02564
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 108 -
Rwork0.226 1786 -
obs--99.32 %

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