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- PDB-3qe4: An evolved aminoacyl-tRNA Synthetase with atypical polysubstrate ... -

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Basic information

Entry
Database: PDB / ID: 3qe4
TitleAn evolved aminoacyl-tRNA Synthetase with atypical polysubstrate specificity
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / evolved tRNA synthetase / tRNA synthetase evolved to bind unnatural amino acids / tRNA
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. / HUPs ...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-cyano-L-phenylalanine / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYoung, D.D. / Young, T.S. / Jahnz, M. / Ahmad, I. / Spraggon, G. / Schultz, P.G.
CitationJournal: Biochemistry / Year: 2011
Title: An Evolved Aminoacyl-tRNA Synthetase with Atypical Polysubstrate Specificity .
Authors: Young, D.D. / Young, T.S. / Jahnz, M. / Ahmad, I. / Spraggon, G. / Schultz, P.G.
History
DepositionJan 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 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
B: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9084
Polymers71,5282
Non-polymers3802
Water3,117173
1
A: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9542
Polymers35,7641
Non-polymers1901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9542
Polymers35,7641
Non-polymers1901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.524, 68.937, 82.089
Angle α, β, γ (deg.)90.00, 90.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35763.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0389, TyrRS, tyrS / Production host: Escherichia coli (E. coli) / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-4CF / 4-cyano-L-phenylalanine


Type: L-peptide linking / Mass: 190.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.2 M ammonium tartrate, 20% PEG3350, 20 mM Tris-HCl, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9778
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. all: 25170 / Num. obs: 25170 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 36.47 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 16.9

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
BUSTER2.9.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J1U

1j1u


Resolution: 2.3→44.45 Å / Cor.coef. Fo:Fc: 0.8964 / Cor.coef. Fo:Fc free: 0.8532 / SU R Cruickshank DPI: 0.564 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / SU R Blow DPI: 0.547 / SU Rfree Blow DPI: 0.317 / SU Rfree Cruickshank DPI: 0.324 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1282 5.09 %RANDOM
Rwork0.233 ---
obs0.2369 25169 96 %-
Displacement parametersBiso mean: 46.59 Å2
Baniso -1Baniso -2Baniso -3
1-12.5354 Å20 Å21.1378 Å2
2---17.4246 Å20 Å2
3---4.8892 Å2
Refine analyzeLuzzati coordinate error obs: 0.364 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4910 0 28 173 5111
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115024HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.286747HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1867SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes134HARMONIC2
X-RAY DIFFRACTIONt_gen_planes703HARMONIC5
X-RAY DIFFRACTIONt_it4996HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion21.3
X-RAY DIFFRACTIONt_chiral_improper_torsion642SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6145SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.39 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2793 111 4.6 %
Rwork0.2242 2304 -
all0.2268 2415 -
obs--96 %
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)
12.5247-0.45691.23340.5977-0.16941.47210.13050.1439-0.0656-0.0989-0.07550.03490.11540.0294-0.0550.0470.0018-0.1511-0.24190-0.04456.27510.498521.8284
21.8873-0.22580.96160.62670.04471.3146-0.01430.1617-0.0183-0.0738-0.01560.0277-0.00730.1170.0299-0.00210.0108-0.1248-0.1751-0.0041-0.03539.5184-33.869921.2302
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|307 }A1 - 307
2X-RAY DIFFRACTION2{ B|2 - B|307 }B2 - 307

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