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- PDB-4s02: Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus... -

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Basic information

Entry
Database: PDB / ID: 4s02
TitleBiphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, F42W, Y79A, and F123Y mutant
ComponentsThreonine--tRNA ligase
KeywordsLIGASE / beta-alpha-beta fold / editing domain / tRNA-synthetase / Biphenylalanine and unnatural amino acid / threonine-tRNA ligase
Function / homology
Function and homology information


threonine-tRNA ligase / threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / tRNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Threonyl-tRNA synthetase, editing domain, archaea / Archaea-specific editing domain of threonyl-tRNA synthetase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / : / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) ...Threonyl-tRNA synthetase, editing domain, archaea / Archaea-specific editing domain of threonyl-tRNA synthetase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / Threonine-tRNA ligase, class IIa / Threonine-tRNA ligase catalytic core domain / : / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Threonine--tRNA ligase
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPearson, A.D. / Mills, J.H. / Song, Y. / Nasertorabi, F. / Han, G.W. / Baker, D. / Stevens, R.C. / Schultz, P.G.
CitationJournal: Science / Year: 2015
Title: Transition states. Trapping a transition state in a computationally designed protein bottle.
Authors: Pearson, A.D. / Mills, J.H. / Song, Y. / Nasertorabi, F. / Han, G.W. / Baker, D. / Stevens, R.C. / Schultz, P.G.
History
DepositionDec 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7514
Polymers17,4331
Non-polymers3183
Water1,24369
1
A: Threonine--tRNA ligase
hetero molecules

A: Threonine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5038
Polymers34,8662
Non-polymers6376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_585-x,-y+3,z1
Unit cell
Length a, b, c (Å)52.715, 77.284, 93.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

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Components

#1: Protein Threonine--tRNA ligase / Threonyl-tRNA synthetase / ThrRS


Mass: 17433.014 Da / Num. of mol.: 1 / Fragment: threonyl-tRNA synthetase / Mutation: I11BIF, F42W, Y79A, F123Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / Gene: PAB1490, PYRAB13430, thrS / Plasmid: pET-22b and pULTRA / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3) / References: UniProt: Q9UZ14, threonine-tRNA ligase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium citrate, 15% PEG 6000, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 14118 / % possible obs: 99.5 % / Redundancy: 11 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 16.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 8.1 / Num. unique all: 2030 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1y2q

1y2q


Resolution: 1.95→24.1 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.245 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19595 709 5 %RANDOM
Rwork0.16333 ---
obs0.1649 13408 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.616 Å2
Baniso -1Baniso -2Baniso -3
1--13.7 Å2-0 Å2-0 Å2
2--2.9 Å20 Å2
3---10.8 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 21 69 1191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191201
X-RAY DIFFRACTIONr_bond_other_d0.0020.021186
X-RAY DIFFRACTIONr_angle_refined_deg1.7972.0011622
X-RAY DIFFRACTIONr_angle_other_deg0.83632739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93324.31451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19115216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.705158
X-RAY DIFFRACTIONr_chiral_restr0.1050.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211336
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02256
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2682.248580
X-RAY DIFFRACTIONr_mcbond_other2.2542.242579
X-RAY DIFFRACTIONr_mcangle_it3.2163.341732
X-RAY DIFFRACTIONr_mcangle_other3.2153.347733
X-RAY DIFFRACTIONr_scbond_it3.9792.935621
X-RAY DIFFRACTIONr_scbond_other3.9722.936621
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1024.149891
X-RAY DIFFRACTIONr_long_range_B_refined8.70120.3291346
X-RAY DIFFRACTIONr_long_range_B_other8.70320.3491347
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 58 -
Rwork0.158 973 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: 1.9835 Å / Origin y: 104.3249 Å / Origin z: 19.2131 Å
111213212223313233
T0.0116 Å20.0158 Å2-0.0021 Å2-0.0592 Å2-0.0092 Å2--0.0177 Å2
L1.5311 °2-0.4788 °2-0.0108 °2-1.187 °2-0.5723 °2--0.7427 °2
S-0.0839 Å °-0.078 Å °-0.0664 Å °0.083 Å °-0.017 Å °-0.0407 Å °-0.0346 Å °-0.0333 Å °0.1009 Å °

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