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- PDB-3ko4: Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium fa... -

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Basic information

Entry
Database: PDB / ID: 3ko4
TitleCrystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium falciparum in complex with ADP
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / DTD / Deacylase / ADP
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
ADENOSINE-5'-DIPHOSPHATE / D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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)116,6809
Polymers115,3996
Non-polymers1,2823
Water18010
1
A: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8933
Polymers38,4662
Non-polymers4271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-8 kcal/mol
Surface area13890 Å2
MethodPISA
2
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3214
Polymers38,4662
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-13 kcal/mol
Surface area13950 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 area3680 Å2
ΔGint-8 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.174, 53.005, 90.432
Angle α, β, γ (deg.)72.860, 76.450, 88.320
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.97 Å3/Da / Density % sol: 37.65 % / Mosaicity: 0.943 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350. 0.1 MES , pH 6.2-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 6.2-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 19638 / % possible obs: 81.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.08 / Χ2: 0.876 / Net I/σ(I): 6.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.387 / Num. unique all: 1080 / Χ2: 0.729 / % possible all: 44.9

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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: 2.7→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.874 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 19.624 / SU ML: 0.408 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1013 5.2 %RANDOM
Rwork0.21 ---
obs0.214 19597 81.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.17 Å2 / Biso mean: 57.401 Å2 / Biso min: 29.97 Å2
Baniso -1Baniso -2Baniso -3
1-3.05 Å2-0.53 Å2-5.23 Å2
2---4.36 Å20.04 Å2
3---3.78 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7458 0 81 10 7549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227685
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9610386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.34725.381381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.961151439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4551530
X-RAY DIFFRACTIONr_chiral_restr0.0850.21158
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025657
X-RAY DIFFRACTIONr_nbd_refined0.2210.23625
X-RAY DIFFRACTIONr_nbtor_refined0.3160.25046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2301
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3110.24
X-RAY DIFFRACTIONr_mcbond_it0.5221.54585
X-RAY DIFFRACTIONr_mcangle_it0.95127296
X-RAY DIFFRACTIONr_scbond_it0.91433517
X-RAY DIFFRACTIONr_scangle_it1.4954.53088
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 43 -
Rwork0.308 678 -
all-721 -
obs--41.06 %

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