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- PDB-5j61: D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in co... -

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Basic information

Entry
Database: PDB / ID: 5j61
TitleD-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with glycyl-3'-aminoadenosine at 2.10 Angstrom resolution
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / DTD / proofreading / chiral / enantioselection
Function / homology
Function and homology information


Gly-tRNA(Ala) deacylase activity / D-tyrosyl-tRNA(Tyr) deacylase activity / D-aminoacyl-tRNA deacylase / tRNA metabolic process / tRNA binding / nucleotide binding / cytoplasm
Similarity search - Function
D-aminoacyl-tRNA deacylase DTD / D-Tyr-tRNA(Tyr) deacylase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3'-deoxy-3'-(glycylamino)adenosine / D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRouth, S.B. / Ahmad, S. / Sankaranarayanan, R.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: Plos Biol. / Year: 2016
Title: Elongation Factor Tu Prevents Misediting of Gly-tRNA(Gly) Caused by the Design Behind the Chiral Proofreading Site of D-Aminoacyl-tRNA Deacylase
Authors: Routh, S.B. / Pawar, K.I. / Ahmad, S. / Singh, S. / Suma, K. / Kumar, M. / Kuncha, S.K. / Yadav, K. / Kruparani, S.P. / Sankaranarayanan, R.
History
DepositionApr 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase
E: D-tyrosyl-tRNA(Tyr) deacylase
F: D-tyrosyl-tRNA(Tyr) deacylase
G: D-tyrosyl-tRNA(Tyr) deacylase
H: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,45116
Polymers153,8658
Non-polymers2,5868
Water3,225179
1
A: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1134
Polymers38,4662
Non-polymers6472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-8 kcal/mol
Surface area13610 Å2
MethodPISA
2
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1134
Polymers38,4662
Non-polymers6472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-8 kcal/mol
Surface area13880 Å2
MethodPISA
3
E: D-tyrosyl-tRNA(Tyr) deacylase
F: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1134
Polymers38,4662
Non-polymers6472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-8 kcal/mol
Surface area13590 Å2
MethodPISA
4
G: D-tyrosyl-tRNA(Tyr) deacylase
H: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1134
Polymers38,4662
Non-polymers6472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-6 kcal/mol
Surface area13530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.156, 86.439, 138.163
Angle α, β, γ (deg.)90.00, 96.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19233.084 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF11_0095 / Plasmid: PET-21B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8IIS0, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-A3G / 3'-deoxy-3'-(glycylamino)adenosine


Mass: 323.308 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H17N7O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG 3350, 0.4M sodium chloride, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 75606 / % possible obs: 96.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.876

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Processing

Software
NameVersionClassification
HKL-2000data processing
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0073refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KNF

3knf


Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.627 / SU ML: 0.237 / Cross valid method: FREE R-VALUE / ESU R: 0.281 / ESU R Free: 0.223
RfactorNum. reflection% reflectionSelection details
Rfree0.26963 3690 4.9 %RANDOM
Rwork0.2201 ---
obs0.22251 71448 96.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.333 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-2.31 Å2
2--0.68 Å2-0 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10044 0 184 179 10407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0210428
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210227
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.97114063
X-RAY DIFFRACTIONr_angle_other_deg0.6943.00323366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2751198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.68825.478513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.107151982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2791540
X-RAY DIFFRACTIONr_chiral_restr0.0690.21564
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022374
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_it2.9835.6644864
X-RAY DIFFRACTIONr_mcbond_other2.9835.6644863
X-RAY DIFFRACTIONr_mcangle_it4.4298.4616038
X-RAY DIFFRACTIONr_mcangle_other4.4298.4626039
X-RAY DIFFRACTIONr_scbond_it3.0676.1345564
X-RAY DIFFRACTIONr_scbond_other3.0676.1345564
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9669.0418025
X-RAY DIFFRACTIONr_long_range_B_refined7.2345.15311553
X-RAY DIFFRACTIONr_long_range_B_other7.22145.13811547
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å /
Num. reflection% reflection
Rwork5384 -
obs-99.21 %

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