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- PDB-5zkf: Crystal Structure of N-terminal Domain of Plasmodium vivax p43 in... -

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Basic information

Entry
Database: PDB / ID: 5zkf
TitleCrystal Structure of N-terminal Domain of Plasmodium vivax p43 in space group P21
ComponentsAminoacyl tRNA Synthetase Complex-Interacting Multifunctional Protein p43
KeywordsLIGASE / GST-like domain / AIMP1 / Plasmodium
Function / homology
Function and homology information


ligase activity / tRNA binding / protein-containing complex
Similarity search - Function
: / : / Nuclear-export cofactor Arc1p / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Glutathione S-transferase, C-terminal domain superfamily / Nucleic acid-binding, OB-fold
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: 2.75 Å
AuthorsGupta, S. / Sharma, M. / Harlos, K. / 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 1.2Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Aminoacyl tRNA Synthetase Complex-Interacting Multifunctional Protein p43
A: Aminoacyl tRNA Synthetase Complex-Interacting Multifunctional Protein p43
C: Aminoacyl tRNA Synthetase Complex-Interacting Multifunctional Protein p43
D: Aminoacyl tRNA Synthetase Complex-Interacting Multifunctional Protein p43


Theoretical massNumber of molelcules
Total (without water)87,2454
Polymers87,2454
Non-polymers00
Water54030
1
B: Aminoacyl tRNA Synthetase Complex-Interacting Multifunctional Protein p43
A: Aminoacyl tRNA Synthetase Complex-Interacting Multifunctional Protein p43


Theoretical massNumber of molelcules
Total (without water)43,6232
Polymers43,6232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-13 kcal/mol
Surface area16990 Å2
MethodPISA
2
C: Aminoacyl tRNA Synthetase Complex-Interacting Multifunctional Protein p43

D: Aminoacyl tRNA Synthetase Complex-Interacting Multifunctional Protein p43


Theoretical massNumber of molelcules
Total (without water)43,6232
Polymers43,6232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1720 Å2
ΔGint-11 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.181, 86.942, 78.411
Angle α, β, γ (deg.)90.000, 91.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aminoacyl tRNA Synthetase Complex-Interacting Multifunctional Protein p43 / tRNA import protein tRIP / putative / Methionine-tRNA ligase / putative


Mass: 21811.281 Da / Num. of mol.: 4 / Fragment: N-terminal 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 40.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium citrate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.748→45.35 Å / Num. obs: 18633 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 1 / Net I/σ(I): 5.4
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 844 / CC1/2: 0.4 / % possible all: 89.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→43.36 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.3581 / WRfactor Rwork: 0.2692 / FOM work R set: 0.7509 / SU B: 40.205 / SU ML: 0.353 / SU Rfree: 0.1007 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2785 1850 10 %RANDOM
Rwork0.2146 ---
obs0.221 16565 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.51 Å2 / Biso mean: 58.312 Å2 / Biso min: 29.96 Å2
Baniso -1Baniso -2Baniso -3
1--32.49 Å2-0 Å2-32.5 Å2
2--3.35 Å2-0 Å2
3---29.14 Å2
Refinement stepCycle: final / Resolution: 2.75→43.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5748 0 0 30 5778
Biso mean---46.82 -
Num. residues----686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195882
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9697911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5275680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11324.912283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.255151146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6011516
X-RAY DIFFRACTIONr_chiral_restr0.090.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024292
LS refinement shellResolution: 2.748→2.819 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 126 -
Rwork0.356 1113 -
all-1239 -
obs--90.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5316-0.03110.57771.68050.26440.7325-0.03150.16560.07440.0823-0.0060.0306-0.01430.04640.03750.06760.00560.05810.0680.01710.058618.991-3.3836.216
21.3507-0.6045-0.14160.8106-0.00690.75480.04080.0014-0.1222-0.0172-0.0587-0.0899-0.1248-0.01640.01790.0281-0.02040.0030.0937-0.00620.066443.716-12.34944.569
31.90520.64440.90960.8971-0.21931.104-0.03770.14580.0620.0506-0.01160.06020.06520.07460.04930.08270.0030.02480.1268-0.01810.015615.373-17.673.006
41.4407-0.0382-0.65191.24110.25741.2251-0.0151-0.0696-0.04980.070.0193-0.0190.05610.0094-0.00430.02960.01340.00120.10050.01060.003443.863-26.53381.586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 174
2X-RAY DIFFRACTION2A1 - 174
3X-RAY DIFFRACTION3C1 - 173
4X-RAY DIFFRACTION4D1 - 174

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