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- PDB-4nbi: D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in co... -

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Basic information

Entry
Database: PDB / ID: 4nbi
TitleD-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at 1.86 Angstrom resolution
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / DTD / DEACYLASE / DTD-like
Function / homology
Function and homology information


Gly-tRNA(Ala) hydrolase 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'-(D-tyrosylamino)adenosine / TRIETHYLENE GLYCOL / D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsAhmad, S. / Routh, S.B. / Kamarthapu, V. / Sankaranarayanan, R.
CitationJournal: Elife / Year: 2013
Title: Mechanism of chiral proofreading during translation of the genetic code.
Authors: Ahmad, S. / Routh, S.B. / Kamarthapu, V. / Chalissery, J. / Muthukumar, S. / Hussain, T. / Kruparani, S.P. / Deshmukh, M.V. / Sankaranarayanan, R.
History
DepositionOct 23, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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_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: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4755
Polymers38,4662
Non-polymers1,0093
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-10 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.134, 65.743, 56.917
Angle α, β, γ (deg.)90.000, 93.300, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 19233.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: DTD, PF11_0095 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8IIS0, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-D3Y / 3'-deoxy-3'-(D-tyrosylamino)adenosine


Mass: 429.430 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O5
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 1.99 Å3/Da / Density % sol: 38.32 % / Mosaicity: 1.277 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 32% PEG 3350, 0.6M sodium chloride, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Aug 21, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→25 Å / Num. obs: 25156 / % possible obs: 98.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.075 / Χ2: 1.343 / Net I/σ(I): 24.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.86-1.936.40.28322830.859189.3
1.93-27.10.23724800.975198.1
2-2.097.10.19125251.083198.4
2.09-2.217.10.15325231.068198.8
2.21-2.347.20.12425041.233199.1
2.34-2.527.20.10225321.294199.5
2.52-2.787.20.07825691.334199.7
2.78-3.187.30.05825521.4841100
3.18-47.20.05125741.9291100
4-257.20.07626142.003199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KNF

3knf


Resolution: 1.86→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.651 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 1276 5.1 %RANDOM
Rwork0.1677 ---
obs0.169 25154 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.35 Å2 / Biso mean: 30.665 Å2 / Biso min: 12.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å2-0.58 Å2
2--0 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 1.86→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 72 250 2915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022693
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.9823633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.21325.504129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88115501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.761510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021992
LS refinement shellResolution: 1.861→1.909 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 71 -
Rwork0.236 1619 -
all-1690 -
obs--91.55 %

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