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- PDB-4rr6: N-terminal editing domain of threonyl-tRNA synthetase from Aeropy... -

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Basic information

Entry
Database: PDB / ID: 4rr6
TitleN-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA (snapshot 1)
ComponentsProbable threonine--tRNA ligase 2
KeywordsLIGASE / DTD-like / Proofreading
Function / homology
Function and homology information


threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / aminoacyl-tRNA deacylase 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 / : / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SERINE-3'-AMINOADENOSINE / Threonine--tRNA ligase editing subunit
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsAhmad, S. / Muthukumar, S. / Yerabham, A.S.K. / Kamarthapu, V. / Sankaranarayanan, R.
CitationJournal: Nat Commun / Year: 2015
Title: Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme.
Authors: Ahmad, S. / Muthukumar, S. / Kuncha, S.K. / Routh, S.B. / Yerabham, A.S. / Hussain, T. / Kamarthapu, V. / Kruparani, S.P. / Sankaranarayanan, R.
History
DepositionNov 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Probable threonine--tRNA ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4892
Polymers15,1351
Non-polymers3531
Water2,756153
1
A: Probable threonine--tRNA ligase 2
hetero molecules

A: Probable threonine--tRNA ligase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9774
Polymers30,2712
Non-polymers7072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3640 Å2
ΔGint-2 kcal/mol
Surface area11460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.956, 46.956, 112.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-744-

HOH

21A-750-

HOH

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Components

#1: Protein Probable threonine--tRNA ligase 2 / Threonyl-tRNA synthetase 2 / ThrRS 2


Mass: 15135.413 Da / Num. of mol.: 1 / Fragment: UNP residues 1-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix K1 (archaea)
Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
Gene: thrS2, APE_0117.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YFY3, threonine-tRNA ligase
#2: Chemical ChemComp-A3S / SERINE-3'-AMINOADENOSINE / N'-L-SERYL-3'-AMINO-(3'-DEOXY)-ADENOSINE


Mass: 353.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, 0.2M MgCl2, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 17, 2011
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→25 Å / Num. obs: 10328 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
AUTOMARdata collection
MOLREPphasing
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.563 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.165 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22119 523 4.8 %RANDOM
Rwork0.17887 ---
obs0.18084 10328 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.836 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.88→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 0 25 153 1246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221124
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9971529
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.28721.59144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04815175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.867158
X-RAY DIFFRACTIONr_chiral_restr0.1030.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022853
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8821.5688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63221108
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.823436
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4814.5421
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 26 -
Rwork0.339 725 -
obs--99.87 %

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