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- PDB-3ko7: DTD from Plasmodium falciparum in complex with D-Lysine -

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Basic information

Entry
Database: PDB / ID: 3ko7
TitleDTD from Plasmodium falciparum in complex with D-Lysine
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / DTD / DEACYLASE / D-AMINO ACID / D-LYSINE
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
D-LYSINE / D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 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 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5457
Polymers115,3996
Non-polymers1461
Water1,04558
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-7 kcal/mol
Surface area14820 Å2
MethodPISA
2
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6123
Polymers38,4662
Non-polymers1461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-8 kcal/mol
Surface area13380 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-7 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.905, 53.238, 91.092
Angle α, β, γ (deg.)74.800, 75.450, 86.070
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
#2: Chemical ChemComp-DLY / D-LYSINE / Lysine


Type: D-peptide linking / Mass: 146.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.04 Å3/Da / Density % sol: 39.63 % / Mosaicity: 0.977 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 1500, 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: Oct 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 43292 / % possible obs: 94.7 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.042 / Χ2: 1.165 / Net I/σ(I): 13.3
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.465 / Num. unique all: 3710 / Χ2: 1.448 / % possible all: 81.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PfDTD-Iodide model (not deposited)

Resolution: 2.21→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 12.762 / SU ML: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.429 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2181 5 %RANDOM
Rwork0.222 ---
obs0.226 43289 95.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.78 Å2 / Biso mean: 60.5 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å20.98 Å2-2.11 Å2
2---1.25 Å23.22 Å2
3---2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7466 0 10 58 7534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227690
X-RAY DIFFRACTIONr_angle_refined_deg1.231.94810368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4645908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.43925.438388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.656151466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0981531
X-RAY DIFFRACTIONr_chiral_restr0.0830.21153
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025695
X-RAY DIFFRACTIONr_nbd_refined0.2030.23398
X-RAY DIFFRACTIONr_nbtor_refined0.3090.25045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.27
X-RAY DIFFRACTIONr_mcbond_it0.6761.54642
X-RAY DIFFRACTIONr_mcangle_it1.21427376
X-RAY DIFFRACTIONr_scbond_it1.16933432
X-RAY DIFFRACTIONr_scangle_it1.8684.52990
LS refinement shellResolution: 2.213→2.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 137 -
Rwork0.386 2686 -
all-2823 -
obs--84.67 %

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