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- PDB-4hk4: Crystal structure of apo Tyrosine-tRNA ligase mutant protein -

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Basic information

Entry
Database: PDB / ID: 4hk4
TitleCrystal structure of apo Tyrosine-tRNA ligase mutant protein
ComponentsTyrosine--tRNA ligase
KeywordsLIGASE / 3-o-methyl tyrosine incorporation into peptide / 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
DI(HYDROXYETHYL)ETHER / Tyrosine--tRNA ligase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å
AuthorsYu, Y. / Zhou, Q. / Dong, J. / Li, J. / Xiaoxuan, L. / Mukherjee, A. / Ouyang, H. / Nilges, M. / Li, H. / Gao, F. ...Yu, Y. / Zhou, Q. / Dong, J. / Li, J. / Xiaoxuan, L. / Mukherjee, A. / Ouyang, H. / Nilges, M. / Li, H. / Gao, F. / Gong, W. / Lu, Y. / Wang, J.
CitationJournal: To be Published
Title: Crystal structure of apo Tyrosine-tRNA ligase mutant protein
Authors: Yu, Y. / Zhou, Q. / Dong, J. / Li, J. / Xiaoxuan, L. / Mukherjee, A. / Ouyang, H. / Nilges, M. / Li, H. / Gao, F. / Gong, W. / Lu, Y. / Wang, J.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Structure summary
Revision 1.2May 27, 2015Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8503
Polymers35,6371
Non-polymers2122
Water543
1
A: Tyrosine--tRNA ligase
hetero molecules

A: Tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6996
Polymers71,2752
Non-polymers4244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4110 Å2
ΔGint-11 kcal/mol
Surface area27280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.695, 38.886, 83.061
Angle α, β, γ (deg.)90.00, 90.98, 90.00
Int Tables number3
Space group name H-MP121

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Components

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


Mass: 35637.297 Da / Num. of mol.: 1 / Mutation: Y32E, L65S, H70G, Q109G, D158N, L162V
Source method: isolated from a genetically manipulated source
Details: restriction endonuclease cleavage sites: NdeI and XhoI
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: tyrS, MJ0389 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q57834, tyrosine-tRNA ligase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: protein sample (40mg/ml) in 25mM Tris-Cl PH8.0, 50mM NaCl mixed with equal volume of reservior solution containing 20-22% PEG3350, 0.2M (NH4)2SO4, 0.1M sodium citrate PH6.1-6.2, for 5 days, ...Details: protein sample (40mg/ml) in 25mM Tris-Cl PH8.0, 50mM NaCl mixed with equal volume of reservior solution containing 20-22% PEG3350, 0.2M (NH4)2SO4, 0.1M sodium citrate PH6.1-6.2, for 5 days, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 15316 / Num. obs: 14520 / % possible obs: 94.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 30.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.97 / % possible all: 70.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J1U

1j1u


Resolution: 2.298→31.287 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 30.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2766 715 5.02 %
Rwork0.229 --
obs0.2314 14240 92.95 %
all-14520 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.968 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.0996 Å2-0 Å2-6.925 Å2
2--8.8821 Å20 Å2
3---2.2175 Å2
Refinement stepCycle: LAST / Resolution: 2.298→31.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 14 3 2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022530
X-RAY DIFFRACTIONf_angle_d0.6623394
X-RAY DIFFRACTIONf_dihedral_angle_d12.7071000
X-RAY DIFFRACTIONf_chiral_restr0.041374
X-RAY DIFFRACTIONf_plane_restr0.002436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2981-2.47540.3556940.26532173X-RAY DIFFRACTION75
2.4754-2.72440.33421690.26972721X-RAY DIFFRACTION95
2.7244-3.11840.34781490.27982794X-RAY DIFFRACTION96
3.1184-3.92760.26061520.24612854X-RAY DIFFRACTION98
3.9276-31.29020.23351510.1862983X-RAY DIFFRACTION99

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