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- PDB-1q11: Crystal structure of an active fragment of human tyrosyl-tRNA syn... -

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Basic information

Entry
Database: PDB / ID: 1q11
TitleCrystal structure of an active fragment of human tyrosyl-tRNA synthetase with tyrosinol
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / Rossmann fold domain containing the active site / anticodon recognition domain / substrate analog tyrosinol co-crystalized
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 / 4-[(2S)-2-amino-3-hydroxypropyl]phenol / Tyrosine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYang, X.-L. / Schimmel, P. / Ribas de Pouplana, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains
Authors: Yang, X.-L. / Otero, F.J. / Skene, R.J. / McRee, D.E. / Schimmel, P. / Ribas De Pouplana, L.
History
DepositionJul 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 17, 2018Group: Data collection / Structure summary / Category: chem_comp
Item: _chem_comp.mon_nstd_flag / _chem_comp.pdbx_synonyms / _chem_comp.type
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / 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: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_conn.ptnr2_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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)42,6196
Polymers42,1341
Non-polymers4855
Water6,269348
1
A: Tyrosyl-tRNA synthetase
hetero molecules

A: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,23812
Polymers84,2672
Non-polymers97110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area4870 Å2
ΔGint-37 kcal/mol
Surface area29160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.825, 162.989, 35.267
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-1097-

HOH

Detailsasymmetric unit contains a monomer of the biologically dimer

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 42133.559 Da / Num. of mol.: 1 / Fragment: mini TyrRS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET20b / Production host: Escherichia coli (E. coli) / References: UniProt: P54577, tyrosine-tRNA ligase

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Non-polymers , 5 types, 353 molecules

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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-TYE / 4-[(2S)-2-amino-3-hydroxypropyl]phenol / tyrosinol / bound form of TYROSINAL / Tyrosinol


Type: L-peptide linking / Mass: 167.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO2
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: (NH4)2SO4, NAH2PO4, K2HPO4, ACETONE, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 %PEG80001reservoir
20.1 Msodium-MES1reservoirpH6.32
310 mMHEPES1droppH7.5
420 mM1dropKCl
50.02 %1dropNaN3
62 mM2-mercaptoethanol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.28 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 58862 / Num. obs: 53993 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 16.2
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.301 / % possible all: 64.5
Reflection
*PLUS
Num. obs: 55381 / % possible obs: 93.8 % / Redundancy: 6.7 %
Reflection shell
*PLUS
% possible obs: 64.5 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N3L, mini TyrRS alone

1n3l


Resolution: 1.6→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2732 -random
Rwork0.1966 ---
obs0.1966 53993 91.7 %-
all-58862 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.842 Å20 Å20 Å2
2--2.658 Å20 Å2
3---0.184 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 30 348 3008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.1
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS

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