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- PDB-4s03: Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus... -

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Basic information

Entry
Database: PDB / ID: 4s03
TitleBiphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: I11BIF, Y79I, and F123A 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
Threonine--tRNA ligase
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)17,3441
Polymers17,3441
Non-polymers00
Water2,792155
1
A: Threonine--tRNA ligase

A: Threonine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)34,6882
Polymers34,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_345-x-2,-y-1,z1
Buried area1700 Å2
ΔGint-6 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.506, 79.098, 91.273
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-248-

HOH

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Components

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


Mass: 17343.961 Da / Num. of mol.: 1 / Fragment: threonyl-tRNA synthetase / Mutation: I11BIF, Y79I, F123A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.75
Details: 0.1 M sodium citrate, 15% PEG 6000, pH 4.75, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 12224 / % possible obs: 99.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.6
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.3 / Num. unique all: 930 / % possible all: 78.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.8.0073refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1y2q

1y2q


Resolution: 2.05→31.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.642 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19939 586 4.8 %RANDOM
Rwork0.16605 ---
obs0.16757 11638 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.504 Å2
Baniso -1Baniso -2Baniso -3
1--4.9 Å2-0 Å2-0 Å2
2---6.92 Å2-0 Å2
3---11.82 Å2
Refinement stepCycle: LAST / Resolution: 2.05→31.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 0 155 1274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191168
X-RAY DIFFRACTIONr_bond_other_d0.0010.021145
X-RAY DIFFRACTIONr_angle_refined_deg1.621.991583
X-RAY DIFFRACTIONr_angle_other_deg0.81232647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9575144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20524.69449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55515212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.011156
X-RAY DIFFRACTIONr_chiral_restr0.0950.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
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_it1.8331.892573
X-RAY DIFFRACTIONr_mcbond_other1.8351.886572
X-RAY DIFFRACTIONr_mcangle_it2.672.824718
X-RAY DIFFRACTIONr_mcangle_other2.6682.831719
X-RAY DIFFRACTIONr_scbond_it3.1492.332595
X-RAY DIFFRACTIONr_scbond_other3.1472.336596
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9573.334866
X-RAY DIFFRACTIONr_long_range_B_refined7.52518.011429
X-RAY DIFFRACTIONr_long_range_B_other7.3216.6931349
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.049→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 34 -
Rwork0.179 837 -
obs--97.65 %
Refinement TLS params.Method: refined / Origin x: -51.0181 Å / Origin y: -51.3783 Å / Origin z: 201.5102 Å
111213212223313233
T0.0323 Å20.0035 Å20.0088 Å2-0.001 Å2-0.0006 Å2--0.0626 Å2
L0.6366 °2-0.1624 °20.1232 °2-0.5443 °2-0.3203 °2--0.3635 °2
S-0.04 Å °-0.0191 Å °-0.0491 Å °0.0272 Å °0.0048 Å °0.0032 Å °-0.0146 Å °-0.0101 Å °0.0352 Å °

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