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

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Basic information

Entry
Database: PDB / ID: 4nbj
TitleD-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at 2.20 Angstrom resolution
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / DTD / DEACYLASE / DTD-like
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'-(D-tyrosylamino)adenosine / D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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: Refinement description / Category: software
Revision 1.2Nov 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 / 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

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)157,30016
Polymers153,8658
Non-polymers3,4358
Water6,756375
1
A: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3254
Polymers38,4662
Non-polymers8592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-10 kcal/mol
Surface area13930 Å2
MethodPISA
2
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3254
Polymers38,4662
Non-polymers8592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-9 kcal/mol
Surface area13440 Å2
MethodPISA
3
E: D-tyrosyl-tRNA(Tyr) deacylase
F: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3254
Polymers38,4662
Non-polymers8592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-9 kcal/mol
Surface area13600 Å2
MethodPISA
4
G: D-tyrosyl-tRNA(Tyr) deacylase
H: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3254
Polymers38,4662
Non-polymers8592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-7 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.901, 79.907, 95.023
Angle α, β, γ (deg.)90.000, 93.510, 90.000
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 (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.: 8 / Source method: obtained synthetically / Formula: C19H23N7O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.24 Å3/Da / Density % sol: 45.06 % / Mosaicity: 1.551 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 28% PEG 3350, 0.4M sodium chloride, 0.1M BisTris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Apr 16, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 69275 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.118 / Χ2: 1.601 / Net I/σ(I): 23
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.285.90.59369111.211199.9
2.28-2.375.80.84268681.197199.9
2.37-2.485.90.5568741.2311100
2.48-2.616.10.44168861.28199.9
2.61-2.776.20.33269351.3671100
2.77-2.986.40.25368741.4971100
2.98-3.286.80.16569481.6271100
3.28-3.767.10.11369461.9341100
3.76-4.737.20.07769382.321100
4.73-257.30.08870951.9861100

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Processing

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

3knf


Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.357 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2535 3497 5.1 %RANDOM
Rwork0.1945 ---
obs0.1975 69240 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.53 Å2 / Biso mean: 48.106 Å2 / Biso min: 24.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å2-0.41 Å2
2---0.65 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10096 0 248 375 10719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0210559
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.98214253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33451205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.18825.478513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.735151997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8831540
X-RAY DIFFRACTIONr_chiral_restr0.0990.21585
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027784
LS refinement shellResolution: 2.196→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 244 -
Rwork0.371 4479 -
all-4723 -
obs--95.65 %

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