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- PDB-1zh6: Crystal Structure of p-acetylphenylalanine-tRNA synthetase in com... -

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Basic information

Entry
Database: PDB / ID: 1zh6
TitleCrystal Structure of p-acetylphenylalanine-tRNA synthetase in complex with p-acetylphenylalanine
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / structural plasticity / unnatural amino acid / tRNA synthetase / ketone
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / ATP binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-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, type 3 / Tyrosine-tRNA ligase, archaeal/eukaryotic-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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-ACETYL-L-PHENYLALANINE / BETA-MERCAPTOETHANOL / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / isomorphous with 1ZH0 / Resolution: 2.5 Å
AuthorsTurner, J.M. / Graziano, J. / Spraggon, G. / Schultz, P.G.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Structural characterization of a p-acetylphenylalanyl aminoacyl-tRNA synthetase.
Authors: Turner, J.M. / Graziano, J. / Spraggon, G. / Schultz, P.G.
History
DepositionApr 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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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)36,4634
Polymers36,1001
Non-polymers3633
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Tyrosyl-tRNA synthetase
hetero molecules

A: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9278
Polymers72,2002
Non-polymers7276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area4820 Å2
ΔGint-21 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.362, 103.362, 70.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 36099.922 Da / Num. of mol.: 1 / Mutation: Y32L,D158G,I159C,L162R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: tyrS / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-4AF / 4-ACETYL-L-PHENYLALANINE / P-ACETYLPHENYLALANINE


Type: L-peptide linking / Mass: 207.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO3
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG-300, 5% PEG-8000,10% glycerol 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 13751 / Num. obs: 13751 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 17.9
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1311 / Rsym value: 0.557 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: isomorphous with 1ZH0 / Resolution: 2.5→73.13 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 23.273 / SU ML: 0.253 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.519 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27773 700 5.1 %RANDOM
Rwork0.2094 ---
all0.213 12978 --
obs0.213 12978 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.412 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2--0.85 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→73.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 23 80 2565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222525
X-RAY DIFFRACTIONr_bond_other_d0.0010.022386
X-RAY DIFFRACTIONr_angle_refined_deg1.3732.0043381
X-RAY DIFFRACTIONr_angle_other_deg0.7583.0015572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2185306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55724.732112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.6315506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3331515
X-RAY DIFFRACTIONr_chiral_restr0.080.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02465
X-RAY DIFFRACTIONr_nbd_refined0.2340.2658
X-RAY DIFFRACTIONr_nbd_other0.1830.22558
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21254
X-RAY DIFFRACTIONr_nbtor_other0.0880.21609
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2112
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.24
X-RAY DIFFRACTIONr_mcbond_it1.18621981
X-RAY DIFFRACTIONr_mcbond_other0.1212624
X-RAY DIFFRACTIONr_mcangle_it1.88852465
X-RAY DIFFRACTIONr_scbond_it4.59481139
X-RAY DIFFRACTIONr_scangle_it6.35711916
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 45 -
Rwork0.323 931 -
obs--97.11 %
Refinement TLS params.Method: refined / Origin x: 80.96 Å / Origin y: 41.589 Å / Origin z: 4.797 Å
111213212223313233
T-0.0169 Å2-0.0123 Å20.0054 Å2--0.0567 Å2-0.0092 Å2---0.01 Å2
L1.9629 °20.5222 °20.9409 °2-1.2138 °20.5668 °2--3.2037 °2
S0.086 Å °-0.2577 Å °0.0271 Å °0.1595 Å °-0.0584 Å °-0.1613 Å °0.0025 Å °0.1164 Å °-0.0276 Å °

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