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- PDB-5zkg: Crystal Structure of C-terminal Domain of Plasmodium vivax p43 -

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Basic information

Entry
Database: PDB / ID: 5zkg
TitleCrystal Structure of C-terminal Domain of Plasmodium vivax p43
ComponentsAminoacyl-tRna synthetase-interacting multifunctional protein P43
KeywordsLIGASE / EMAPII-like domain / AIMP1 / Plasmodium
Function / homology
Function and homology information


ligase activity / tRNA binding
Similarity search - Function
: / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Glutathione S-transferase, C-terminal domain superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(malaria parasite P. vivax) hypothetical protein / Methionine-tRNA ligase, putative
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsGupta, S. / Sharma, M. / Manickam, Y. / Sharma, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Crystal structures of the two domains that constitute the Plasmodium vivax p43 protein.
Authors: Gupta, S. / Chhibber-Goel, J. / Sharma, M. / Parvez, S. / Harlos, K. / Sharma, A. / Yogavel, M.
History
DepositionMar 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminoacyl-tRna synthetase-interacting multifunctional protein P43
B: Aminoacyl-tRna synthetase-interacting multifunctional protein P43


Theoretical massNumber of molelcules
Total (without water)45,7442
Polymers45,7442
Non-polymers00
Water00
1
A: Aminoacyl-tRna synthetase-interacting multifunctional protein P43


Theoretical massNumber of molelcules
Total (without water)22,8721
Polymers22,8721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminoacyl-tRna synthetase-interacting multifunctional protein P43


Theoretical massNumber of molelcules
Total (without water)22,8721
Polymers22,8721
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.200, 105.200, 36.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Aminoacyl-tRna synthetase-interacting multifunctional protein P43 / tRNA import protein tRIP / putative


Mass: 22872.205 Da / Num. of mol.: 2 / Fragment: C-terminal EMAP II-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVC01_120068600, PVP01_1264700, PVT01_120069000 / Plasmid: pETM-11 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1G4HHT8, UniProt: A5K3Y7*PLUS

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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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M bicine/Trizma base pH 8.5, 0.02M of alcohols [0.2M 1,6-hexanediol, 0.2M 1-butanol, 0.2M (RS)-1,2propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol], 12.5% w/v PEG ...Details: 0.1M bicine/Trizma base pH 8.5, 0.02M of alcohols [0.2M 1,6-hexanediol, 0.2M 1-butanol, 0.2M (RS)-1,2propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol], 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→47.05 Å / Num. obs: 6367 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.99 / Net I/σ(I): 5.92
Reflection shellResolution: 3.3→3.5 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 0.86 / Num. unique obs: 993 / CC1/2: 0.4 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NTG

1ntg


Resolution: 3.3→47.047 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.44
RfactorNum. reflection% reflection
Rfree0.2778 318 5.01 %
Rwork0.2165 --
obs0.2197 6347 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.47 Å2 / Biso mean: 85.3925 Å2 / Biso min: 46.67 Å2
Refinement stepCycle: final / Resolution: 3.3→47.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 0 0 2344
Num. residues----330
LS refinement shellResolution: 3.2972→4.1537 Å
RfactorNum. reflection% reflection
Rfree0.3102 156 -
Rwork0.2541 --
obs-2962 99 %
Refinement TLS params.Method: refined / Origin x: 136.4627 Å / Origin y: 19.5749 Å / Origin z: 3.397 Å
111213212223313233
T0.5733 Å20.034 Å20.0288 Å2-0.6462 Å20.0085 Å2--0.5749 Å2
L0.8735 °21.0764 °2-0.3574 °2-1.2861 °2-0.6007 °2--0.5929 °2
S-0.0395 Å °-0.1473 Å °-0.0185 Å °0.099 Å °0.0408 Å °0.0037 Å °0.1 Å °0.0664 Å °0.0107 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 164
2X-RAY DIFFRACTION1allB0 - 164

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