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- PDB-4s0i: Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus... -

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Basic information

Entry
Database: PDB / ID: 4s0i
TitleBiphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: 11BIF, 42F, 79S, and 123A 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: 2.36 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 31, 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)17,3181
Polymers17,3181
Non-polymers00
Water23413
1
A: Threonine--tRNA ligase

A: Threonine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)34,6362
Polymers34,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_895-x+3,-y+4,z1
Unit cell
Length a, b, c (Å)52.614, 78.915, 91.063
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-209-

HOH

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Components

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


Mass: 17317.881 Da / Num. of mol.: 1 / Fragment: threonyl-tRNA synthetase / Mutation: I11BIF, Y79S, 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.: 13 / 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: 54.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.75
Details: 0.1M 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: Mar 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: 2.36→50 Å / Num. obs: 8045 / % possible obs: 99.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.3
Reflection shellResolution: 2.36→2.45 Å / Redundancy: 6 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3.3 / Num. unique all: 817 / % possible all: 99.6

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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: 2.36→31.56 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 11.542 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23788 372 4.6 %RANDOM
Rwork0.19004 ---
obs0.19239 7673 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.65 Å2
Baniso -1Baniso -2Baniso -3
1--6 Å2-0 Å2-0 Å2
2---11.61 Å2-0 Å2
3---17.61 Å2
Refinement stepCycle: LAST / Resolution: 2.36→31.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 0 13 1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191151
X-RAY DIFFRACTIONr_bond_other_d0.0010.021134
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.9981555
X-RAY DIFFRACTIONr_angle_other_deg0.93132625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5585142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.83924.79248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96615213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.596156
X-RAY DIFFRACTIONr_chiral_restr0.1120.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02239
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_it2.9652.872568
X-RAY DIFFRACTIONr_mcbond_other2.882.867567
X-RAY DIFFRACTIONr_mcangle_it4.3834.302710
X-RAY DIFFRACTIONr_mcangle_other4.3984.312711
X-RAY DIFFRACTIONr_scbond_it3.8863.38583
X-RAY DIFFRACTIONr_scbond_other3.8833.388584
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0494.885846
X-RAY DIFFRACTIONr_long_range_B_refined7.54222.8511202
X-RAY DIFFRACTIONr_long_range_B_other7.57222.8881203
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.364→2.425 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 29 -
Rwork0.247 546 -
obs--99.31 %
Refinement TLS params.Method: refined / Origin x: 77.0325 Å / Origin y: 169.5895 Å / Origin z: 201.1805 Å
111213212223313233
T0.0262 Å20.0141 Å2-0.0213 Å2-0.0387 Å2-0.0017 Å2--0.0693 Å2
L2.0111 °2-0.4705 °2-0.4569 °2-1.8184 °20.7524 °2--1.0324 °2
S-0.0937 Å °-0.0714 Å °0.0773 Å °0.1445 Å °-0.0053 Å °0.0363 Å °0.0089 Å °0.0054 Å °0.0991 Å °

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