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

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Basic information

Entry
Database: PDB / ID: 3lmu
TitleCrystal structure of DTD from Plasmodium falciparum
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / DTD / IODIDE / 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
IODIDE ION / D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SAD / Resolution: 3.3 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 1.2Sep 5, 2012Group: Derived calculations
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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 1.4Sep 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 1.5Mar 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

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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
G: D-tyrosyl-tRNA(Tyr) deacylase
H: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,16434
Polymers153,8658
Non-polymers3,30026
Water00
1
A: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2288
Polymers38,4662
Non-polymers7616
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-10 kcal/mol
Surface area13130 Å2
MethodPISA
2
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,73512
Polymers38,4662
Non-polymers1,26910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-8 kcal/mol
Surface area12200 Å2
MethodPISA
3
E: D-tyrosyl-tRNA(Tyr) deacylase
F: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1017
Polymers38,4662
Non-polymers6355
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-10 kcal/mol
Surface area11790 Å2
MethodPISA
4
G: D-tyrosyl-tRNA(Tyr) deacylase
H: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1017
Polymers38,4662
Non-polymers6355
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-13 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.18, 77.18, 214.52
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
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
11METMETGLYGLYchain A and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )AA1 - 101 - 10
12ILEILEILEILEchain A and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )AA30 - 5530 - 55
13TYRTYRTHRTHRchain A and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )AA81 - 9081 - 90
14GLUGLUILEILEchain A and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )AA111 - 155111 - 155
21METMETGLYGLYchain B and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )BB1 - 101 - 10
22ILEILEILEILEchain B and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )BB30 - 5530 - 55
23TYRTYRTHRTHRchain B and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )BB81 - 9081 - 90
24GLUGLUILEILEchain B and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )BB111 - 155111 - 155
31METMETGLYGLYchain C and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )CC1 - 101 - 10
32ILEILEILEILEchain C and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )CC30 - 5530 - 55
33TYRTYRTHRTHRchain C and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )CC81 - 9081 - 90
34GLUGLUILEILEchain C and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )CC111 - 155111 - 155
41METMETGLYGLYchain D and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )DD1 - 101 - 10
42ILEILEILEILEchain D and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )DD30 - 5530 - 55
43TYRTYRTHRTHRchain D and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )DD81 - 9081 - 90
44GLUGLUILEILEchain D and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )DD111 - 155111 - 155
51METMETGLYGLYchain E and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )EE1 - 101 - 10
52ILEILEILEILEchain E and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )EE30 - 5530 - 55
53TYRTYRTHRTHRchain E and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )EE81 - 9081 - 90
54GLUGLUILEILEchain E and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )EE111 - 155111 - 155
61METMETGLYGLYchain F and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )FF1 - 101 - 10
62ILEILEILEILEchain F and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )FF30 - 5530 - 55
63TYRTYRTHRTHRchain F and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )FF81 - 9081 - 90
64GLUGLUILEILEchain F and (resseq 1:10 or resseq 30:55 or resseq 81:90 or resseq 111:155 )FF111 - 155111 - 155

NCS oper:
IDCodeMatrixVector
1given(-0.091624, -0.2883, 0.953147), (-0.304625, -0.903171, -0.302466), (0.948055, -0.318065, -0.005071)-28.819401, 58.2952, 45.6642
2given(-0.232799, 0.299865, 0.925141), (0.668606, -0.641459, 0.376161), (0.706237, 0.706124, -0.05116)-72.474197, 47.439701, -20.804199
3given(0.494037, 0.831534, -0.253927), (-0.756603, 0.267289, -0.596748), (-0.428345, 0.486938, 0.761191)-55.405602, 43.757702, -38.1819
4given(0.63094, 0.685332, -0.363641), (-0.698506, 0.297807, -0.650692), (-0.337646, 0.664553, 0.666607)-50.8246, 7.62969, -76.205803
5given(-0.162204, 0.491217, 0.855801), (0.554587, -0.671965, 0.490812), (0.816163, 0.554228, -0.163427)-98.685799, 90.058098, -4.38311

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Components

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


Mass: 19233.084 Da / Num. of mol.: 8
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.: 26 / Source method: obtained synthetically / Formula: I

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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: 2.08 Å3/Da / Density % sol: 40.76 % / Mosaicity: 0.583 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG1500, 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: Jul 29, 2007 / Details: mirrors
RadiationProtocol: 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: 18914 / % possible obs: 100 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.162 / Χ2: 1.328 / Net I/σ(I): 6.8
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.516 / Num. unique all: 1869 / Χ2: 1.125 / % possible all: 100

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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
RefinementMethod to determine structure: SAD / Resolution: 3.3→33.958 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.36 / σ(F): 1.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 971 5.15 %
Rwork0.185 --
obs0.189 18839 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.34 Å2 / ksol: 0.287 e/Å3
Displacement parametersBiso max: 118.19 Å2 / Biso mean: 48.635 Å2 / Biso min: 18.57 Å2
Baniso -1Baniso -2Baniso -3
1--7.12 Å2-0 Å20 Å2
2---7.12 Å20 Å2
3---14.241 Å2
Refinement stepCycle: LAST / Resolution: 3.3→33.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9253 0 26 0 9279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099441
X-RAY DIFFRACTIONf_angle_d1.15412835
X-RAY DIFFRACTIONf_chiral_restr0.071487
X-RAY DIFFRACTIONf_plane_restr0.0031636
X-RAY DIFFRACTIONf_dihedral_angle_d20.2133242
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A720X-RAY DIFFRACTIONPOSITIONAL0.048
12B720X-RAY DIFFRACTIONPOSITIONAL0.048
13C719X-RAY DIFFRACTIONPOSITIONAL0.045
14D716X-RAY DIFFRACTIONPOSITIONAL0.048
15E718X-RAY DIFFRACTIONPOSITIONAL0.05
16F717X-RAY DIFFRACTIONPOSITIONAL0.047
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.298-3.4710.2881440.21425342678100
3.471-3.6890.2781420.19725642706100
3.689-3.9730.2771440.18825142658100
3.973-4.3720.221250.15525952720100
4.372-5.0030.2011390.14825412680100
5.003-6.2970.2591280.18325632691100
6.297-33.960.2661490.1982557270699

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