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- PDB-3knp: Crystal structure of DTD from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 3knp
TitleCrystal structure of DTD from Plasmodium falciparum
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / DTD / 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 / molecular replacement / Resolution: 3.3 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 8, 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

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


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 area3620 Å2
ΔGint-12 kcal/mol
Surface area14840 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 area3650 Å2
ΔGint-9 kcal/mol
Surface area14770 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 area3580 Å2
ΔGint-9 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.810, 55.170, 92.520
Angle α, β, γ (deg.)105.900, 103.100, 98.700
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: 2.37 Å3/Da / Density % sol: 48.16 %

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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 10, 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: 3.3→50 Å / Num. obs: 15063 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.093
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.424 / Num. unique all: 1497 / % possible all: 96.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
CNS1.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PfDTD-Iodide SAD model (not deposited)

Resolution: 3.3→19.87 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 0.4 / Data cutoff high absF: 1519712 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 702 4.7 %RANDOM
Rwork0.214 ---
obs-15011 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.666 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso max: 111.36 Å2 / Biso mean: 69.936 Å2 / Biso min: 0.01 Å2
Baniso -1Baniso -2Baniso -3
1-22.6 Å2-14.54 Å27.92 Å2
2---14.62 Å24.75 Å2
3----7.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 3.3→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7387 0 0 0 7387
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d1.5
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 90 4.5 %
Rwork0.338 1911 -
all-2001 -
obs--76.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2

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