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- PDB-3lmv: D-Tyr-tRNA(Tyr) Deacylase from plasmodium falciparum in complex w... -

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Basic information

Entry
Database: PDB / ID: 3lmv
TitleD-Tyr-tRNA(Tyr) Deacylase from plasmodium falciparum in complex with hepes
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / DTD / HEPES / 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
SULFITE ION / D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.833 Å
AuthorsManickam, Y. / Khan, S. / Bhatt, T.K. / 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
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 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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

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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)116,83014
Polymers115,3996
Non-polymers1,4328
Water00
1
A: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3417
Polymers38,4662
Non-polymers8755
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-8 kcal/mol
Surface area12850 Å2
MethodPISA
2
C: D-tyrosyl-tRNA(Tyr) deacylase
D: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9434
Polymers38,4662
Non-polymers4772
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-7 kcal/mol
Surface area13020 Å2
MethodPISA
3
E: D-tyrosyl-tRNA(Tyr) deacylase
F: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5463
Polymers38,4662
Non-polymers801
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-7 kcal/mol
Surface area11740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.65, 52.95, 89.68
Angle α, β, γ (deg.)75.4, 74.2, 86.1
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 1:16 or resseq 27:65 or resseq 72:161 )A1 - 16
121chain A and (resseq 1:16 or resseq 27:65 or resseq 72:161 )A27 - 65
131chain A and (resseq 1:16 or resseq 27:65 or resseq 72:161 )A72 - 161
211chain B and (resseq 1:16 or resseq 27:65 or resseq 72:161 )B1 - 16
221chain B and (resseq 1:16 or resseq 27:65 or resseq 72:161 )B27 - 65
231chain B and (resseq 1:16 or resseq 27:65 or resseq 72:161 )B72 - 161
311chain C and (resseq 1:16 or resseq 27:65 or resseq 72:161 )C1 - 16
321chain C and (resseq 1:16 or resseq 27:65 or resseq 72:161 )C27 - 65
331chain C and (resseq 1:16 or resseq 27:65 or resseq 72:161 )C72 - 161
411chain D and (resseq 1:16 or resseq 27:65 or resseq 72:161 )D1 - 16
421chain D and (resseq 1:16 or resseq 27:65 or resseq 72:161 )D27 - 65
431chain D and (resseq 1:16 or resseq 27:65 or resseq 72:161 )D72 - 161
511chain E and (resseq 1:16 or resseq 27:65 or resseq 72:161 )E1 - 16
521chain E and (resseq 1:16 or resseq 27:65 or resseq 72:161 )E27 - 65
531chain E and (resseq 1:16 or resseq 27:65 or resseq 72:161 )E72 - 161
611chain F and (resseq 1:16 or resseq 27:65 or resseq 72:161 )F1 - 16
621chain F and (resseq 1:16 or resseq 27:65 or resseq 72:161 )F27 - 65
631chain F and (resseq 1:16 or resseq 27:65 or resseq 72:161 )F72 - 161

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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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO3

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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: 1.98 Å3/Da / Density % sol: 37.85 % / Mosaicity: 1.748 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M TRIS/HEPES, 25-30% PEG3350, pH 7.5-8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 7.5-8.5

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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 29, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. obs: 20391 / % possible obs: 95.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.062 / Χ2: 1.193 / Net I/σ(I): 12.6
Reflection shellResolution: 2.82→2.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.313 / Num. unique all: 1702 / Χ2: 1.365 / % possible all: 79.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.02 Å49.69 Å
Translation3.02 Å49.69 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LMT

3lmt


Resolution: 2.833→29.243 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.38 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 1042 5.11 %
Rwork0.207 --
obs0.209 20373 96.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.546 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 124.27 Å2 / Biso mean: 59.86 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--18.435 Å26.556 Å2-13.409 Å2
2---9.232 Å213.226 Å2
3---27.667 Å2
Refinement stepCycle: LAST / Resolution: 2.833→29.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6960 0 87 0 7047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097171
X-RAY DIFFRACTIONf_angle_d1.0389724
X-RAY DIFFRACTIONf_chiral_restr0.0581109
X-RAY DIFFRACTIONf_plane_restr0.0041221
X-RAY DIFFRACTIONf_dihedral_angle_d20.7072524
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1109X-RAY DIFFRACTIONPOSITIONAL0.056
12B1109X-RAY DIFFRACTIONPOSITIONAL0.056
13C1129X-RAY DIFFRACTIONPOSITIONAL0.055
14D1127X-RAY DIFFRACTIONPOSITIONAL0.052
15E986X-RAY DIFFRACTIONPOSITIONAL0.051
16F1115X-RAY DIFFRACTIONPOSITIONAL0.052
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 (%)
2.832-2.9820.3951450.2912614275992
2.982-3.1680.3351290.2442769289897
3.168-3.4130.2911500.2282759290997
3.413-3.7550.2511530.22792294597
3.755-4.2970.2211410.1822791293298
4.297-5.4090.1911630.1632784294799
5.409-29.2450.2481610.2152822298399

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