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

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Basic information

Entry
Database: PDB / ID: 3lmt
TitleCrystal structure of DTD from Plasmodium falciparum
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / DTD / DEACYLASE / IODIDE
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
IODIDE ION / D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.75 Å
AuthorsManickam, Y. / Bhatt, T.K. / Khan, S. / Sharma, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure of D-tyrosyl-tRNATyr deacylase using home-source Cu Kalpha and moderate-quality iodide-SAD data: structural polymorphism and HEPES-bound enzyme states
Authors: Yogavel, M. / Khan, S. / Bhatt, T.K. / Sharma, A.
History
DepositionFeb 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 16, 2020Group: Derived calculations / Structure summary / Category: struct / struct_site
Item: _struct.title / _struct_site.pdbx_auth_asym_id ..._struct.title / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5May 28, 2025Group: Structure summary / Category: pdbx_entry_details

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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)119,07935
Polymers115,3996
Non-polymers3,68029
Water3,189177
1
A: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,73512
Polymers38,4662
Non-polymers1,26910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,48110
Polymers38,4662
Non-polymers1,0158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: D-tyrosyl-tRNA(Tyr) deacylase
F: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,86213
Polymers38,4662
Non-polymers1,39611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.34, 57.88, 91.63
Angle α, β, γ (deg.)102.8, 105.9, 99.6
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEUchain A and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )AA1 - 131 - 13
12ILEILECYSCYSchain A and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )AA30 - 5930 - 59
13TYRTYRTHRTHRchain A and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )AA81 - 9081 - 90
14GLUGLUILEILEchain A and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )AA111 - 155111 - 155
21METMETLEULEUchain B and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )BB1 - 131 - 13
22ILEILECYSCYSchain B and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )BB30 - 5930 - 59
23TYRTYRTHRTHRchain B and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )BB81 - 9081 - 90
24GLUGLUILEILEchain B and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )BB111 - 155111 - 155
31METMETLEULEUchain C and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )CC1 - 131 - 13
32ILEILECYSCYSchain C and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )CC30 - 5930 - 59
33TYRTYRTHRTHRchain C and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )CC81 - 9081 - 90
34GLUGLUILEILEchain C and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )CC111 - 155111 - 155
41METMETLEULEUchain D and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )DD1 - 131 - 13
42ILEILECYSCYSchain D and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )DD30 - 5930 - 59
43TYRTYRTHRTHRchain D and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )DD81 - 9081 - 90
44GLUGLUILEILEchain D and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )DD111 - 155111 - 155
51METMETLEULEUchain E and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )EE1 - 131 - 13
52ILEILECYSCYSchain E and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )EE30 - 5930 - 59
53TYRTYRTHRTHRchain E and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )EE81 - 9081 - 90
54GLUGLUILEILEchain E and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )EE111 - 155111 - 155
61METMETLEULEUchain F and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )FF1 - 131 - 13
62ILEILECYSCYSchain F and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )FF30 - 5930 - 59
63TYRTYRTHRTHRchain F and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )FF81 - 9081 - 90
64GLUGLUILEILEchain F and (resseq 1:13 or resseq 30:59 or resseq 81:90 or resseq 111:155 )FF111 - 155111 - 155

NCS oper:
IDCodeMatrixVector
1given(0.225888, -0.726788, 0.648656), (-0.721723, -0.572084, -0.38966), (0.654286, -0.38013, -0.653767)-39.316799, 33.341999, 111.078003
2given(-0.807978, 0.553492, 0.202033), (-0.514296, -0.49517, -0.700219), (-0.287525, -0.669666, 0.684745)-17.2794, 8.70734, 19.805599
3given(0.001083, 0.060136, 0.99819), (0.989573, 0.1437, -0.009731), (-0.144025, 0.987792, -0.059354)-36.539799, 33.0382, 84.052002
4given(0.774363, 0.254303, -0.579389), (-0.355006, 0.932592, -0.065142), (0.523767, 0.25613, 0.812444)7.35204, -5.0674, 55.709499
5given(0.768463, -0.462321, 0.442407), (-0.570879, -0.807657, 0.147607), (0.289071, -0.365991, -0.884584)2.23564, 9.12125, 81.554802
DetailsHomo dimer

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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, PF11_0095 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q8IIS0, Hydrolases; Acting on ester bonds
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.85 % / Mosaicity: 0.776 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.1M 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 6, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 26067 / % possible obs: 96.8 % / Redundancy: 8 % / Rmerge(I) obs: 0.095 / Χ2: 2.08 / Net I/σ(I): 13.5
Reflection shellResolution: 2.74→2.84 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.364 / Num. unique all: 2375 / Χ2: 1.453 / % possible all: 89.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.75→29.668 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.36 / σ(F): 1.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1304 5.09 %
Rwork0.181 --
obs0.184 25632 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.848 Å2 / ksol: 0.286 e/Å3
Displacement parametersBiso max: 95.75 Å2 / Biso mean: 38.402 Å2 / Biso min: 15.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.901 Å2-8.379 Å2-4.583 Å2
2---6.97 Å25.233 Å2
3---8.871 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7359 0 29 177 7565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087527
X-RAY DIFFRACTIONf_angle_d1.02510203
X-RAY DIFFRACTIONf_chiral_restr0.0691165
X-RAY DIFFRACTIONf_plane_restr0.0031297
X-RAY DIFFRACTIONf_dihedral_angle_d19.7472685
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A777X-RAY DIFFRACTIONPOSITIONAL0.047
12B777X-RAY DIFFRACTIONPOSITIONAL0.047
13C782X-RAY DIFFRACTIONPOSITIONAL0.042
14D783X-RAY DIFFRACTIONPOSITIONAL0.048
15E765X-RAY DIFFRACTIONPOSITIONAL0.045
16F756X-RAY DIFFRACTIONPOSITIONAL0.046
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.753-2.8640.3411090.2552351246084
2.864-2.9940.3391340.2332732286696
2.994-3.1510.2781510.2192708285996
3.151-3.3490.261480.1962757290597
3.349-3.6070.2291640.1812760292497
3.607-3.9690.2191450.1662735288097
3.969-4.5420.1811400.1422771291198
4.542-5.7150.2041620.1452776293898
5.715-29.6690.231510.1852738288997

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