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- PDB-3knf: Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium fa... -

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Basic information

Entry
Database: PDB / ID: 3knf
TitleCrystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium falciparum
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / D-AMINO ACID / DEACYLASE
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
D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsManickam, Y. / Bhatt, T.K. / Sharma, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Ligand-bound Structures Provide Atomic Snapshots for the Catalytic Mechanism of D-Amino Acid Deacylase
Authors: Bhatt, T.K. / Yogavel, M. / Wydau, S. / Berwal, R. / Sharma, A.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase
E: D-tyrosyl-tRNA(Tyr) deacylase
F: D-tyrosyl-tRNA(Tyr) deacylase


Theoretical massNumber of molelcules
Total (without water)115,3996
Polymers115,3996
Non-polymers00
Water00
1
A: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase


Theoretical massNumber of molelcules
Total (without water)38,4662
Polymers38,4662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-8 kcal/mol
Surface area13570 Å2
MethodPISA
2
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase


Theoretical massNumber of molelcules
Total (without water)38,4662
Polymers38,4662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-9 kcal/mol
Surface area13730 Å2
MethodPISA
3
E: D-tyrosyl-tRNA(Tyr) deacylase
F: D-tyrosyl-tRNA(Tyr) deacylase


Theoretical massNumber of molelcules
Total (without water)38,4662
Polymers38,4662
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-9 kcal/mol
Surface area13620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.323, 53.708, 90.531
Angle α, β, γ (deg.)106.58, 102.29, 90.91
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 19233.084 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: dtd / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q8IIS0, Hydrolases; Acting on ester bonds

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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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 7, 2008 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 18085 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.108
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.563 / Num. unique all: 1777 / % possible all: 96.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PfDTD-Iodide model (not deposited)

Resolution: 3→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.255 966 RANDOM
Rwork0.19 --
all0.193 18035 -
obs-18035 -
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7444 0 0 0 7444
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d1.373

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