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- PDB-5xaq: Crystal structure of Animalia-specific tRNA deacylase from Mus mu... -

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Basic information

Entry
Database: PDB / ID: 5xaq
TitleCrystal structure of Animalia-specific tRNA deacylase from Mus musculus
ComponentsProbable D-tyrosyl-tRNA(Tyr) deacylase 2
KeywordsHYDROLASE / tRNA / deacylase
Function / homology
Function and homology information


Ala-tRNA(Thr) deacylase activity / aminoacyl-tRNA metabolism involved in translational fidelity / D-aminoacyl-tRNA deacylase / D-tyrosyl-tRNA(Tyr) deacylase activity / tRNA metabolic process / tRNA binding / cytoplasm
Similarity search - Function
D-aminoacyl-tRNA deacylase DTD / D-Tyr-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily
Similarity search - Domain/homology
D-aminoacyl-tRNA deacylase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsKuncha, K.S. / Kattula, B. / Sankarnarayanan, R.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: Nat Commun / Year: 2018
Title: A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia
Authors: Kuncha, S.K. / Mazeed, M. / Singh, R. / Kattula, B. / Routh, S.B. / Sankaranarayanan, R.
History
DepositionMar 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable D-tyrosyl-tRNA(Tyr) deacylase 2
B: Probable D-tyrosyl-tRNA(Tyr) deacylase 2


Theoretical massNumber of molelcules
Total (without water)36,5182
Polymers36,5182
Non-polymers00
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-11 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.379, 75.351, 103.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable D-tyrosyl-tRNA(Tyr) deacylase 2 / D-tyrosyl-tRNA deacylase 2


Mass: 18258.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dtd2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q8BHA3, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: BICINE (pH 8.0), PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.86→60.94 Å / Num. obs: 29268 / % possible obs: 89.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 21.8
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.4 / % possible all: 51.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
AUTOMAR0.7data collection
HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
AUTOMARphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NBI

4nbi


Resolution: 1.86→60.94 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.778 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.175 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24967 1262 4.8 %RANDOM
Rwork0.20121 ---
obs0.20357 24840 89.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.403 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å2-0 Å20 Å2
2---0.45 Å2-0 Å2
3----1.98 Å2
Refinement stepCycle: 1 / Resolution: 1.86→60.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 0 219 2719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192540
X-RAY DIFFRACTIONr_bond_other_d0.0020.022486
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.9583435
X-RAY DIFFRACTIONr_angle_other_deg1.08735698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5835325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55824.286112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61715439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1331517
X-RAY DIFFRACTIONr_chiral_restr0.1330.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022902
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02579
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_it2.882.8461306
X-RAY DIFFRACTIONr_mcbond_other2.882.8461305
X-RAY DIFFRACTIONr_mcangle_it3.6194.2561629
X-RAY DIFFRACTIONr_mcangle_other3.6184.2561630
X-RAY DIFFRACTIONr_scbond_it3.9783.3311234
X-RAY DIFFRACTIONr_scbond_other3.9773.3311235
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9834.7841807
X-RAY DIFFRACTIONr_long_range_B_refined7.34923.2842820
X-RAY DIFFRACTIONr_long_range_B_other7.30922.9182729
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.864→1.912 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 80 -
Rwork0.331 1245 -
obs--62.12 %

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