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- PDB-4s0j: Biphenylalanine modified threonyl-tRNA synthetase from Pyrococcus... -

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Basic information

Entry
Database: PDB / ID: 4s0j
TitleBiphenylalanine modified threonyl-tRNA synthetase from Pyrococcus abyssi: 11BIF, 42F, 79S, and 123V 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


threonyl-tRNA aminoacylation / threonine-tRNA ligase / 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: 2.1 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)17,3461
Polymers17,3461
Non-polymers00
Water23413
1
A: Threonine--tRNA ligase

A: Threonine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)34,6922
Polymers34,6922
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 area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.285, 78.963, 90.558
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 17345.936 Da / Num. of mol.: 1 / Fragment: threonyl-tRNA synthetase / Mutation: I11BIF, Y79S, F123V
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 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M 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: 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: 2.1→50 Å / Num. obs: 11173 / % possible obs: 98.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.1 / Num. unique all: 896 / % possible all: 98.5

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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: 2.1→39.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.852 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21119 535 4.8 %RANDOM
Rwork0.19775 ---
obs0.19843 10638 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.837 Å2
Baniso -1Baniso -2Baniso -3
1--12.98 Å2-0 Å2-0 Å2
2---7.18 Å2-0 Å2
3---20.16 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1115 0 0 13 1128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191154
X-RAY DIFFRACTIONr_bond_other_d0.0010.021134
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.9971558
X-RAY DIFFRACTIONr_angle_other_deg0.87332628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9985143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84724.89849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58515217
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.848156
X-RAY DIFFRACTIONr_chiral_restr0.110.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211283
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
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_it2.7123.11569
X-RAY DIFFRACTIONr_mcbond_other2.7163.105568
X-RAY DIFFRACTIONr_mcangle_it3.6614.65713
X-RAY DIFFRACTIONr_mcangle_other3.6614.655714
X-RAY DIFFRACTIONr_scbond_it4.033.608585
X-RAY DIFFRACTIONr_scbond_other4.0263.611586
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8895.212846
X-RAY DIFFRACTIONr_long_range_B_refined7.32325.2371241
X-RAY DIFFRACTIONr_long_range_B_other7.32125.2591242
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.097→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 30 -
Rwork0.264 778 -
obs--98.3 %
Refinement TLS params.Method: refined / Origin x: -50.3571 Å / Origin y: -51.1876 Å / Origin z: 200.0314 Å
111213212223313233
T0.0167 Å20.0072 Å20.0062 Å2-0.0145 Å2-0.0118 Å2--0.0693 Å2
L1.554 °2-0.7342 °20.2506 °2-1.4462 °2-0.6791 °2--0.718 °2
S-0.1254 Å °-0.0674 Å °-0.0159 Å °0.1283 Å °0.0199 Å °0.0008 Å °-0.0479 Å °-0.0021 Å °0.1055 Å °

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