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- PDB-6jre: Structure of N-terminal domain of Plasmodium vivax p43 (PfNTD) so... -

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Basic information

Entry
Database: PDB / ID: 6jre
TitleStructure of N-terminal domain of Plasmodium vivax p43 (PfNTD) solved by Co-SAD phasing
ComponentsAminoacyl-tRNA synthetase-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
: / Methionine-tRNA ligase / (malaria parasite P. vivax) hypothetical protein
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
AuthorsManickam, Y. / Harlos, K. / Sharma, M. / Gupta, S. / Sharma, A.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)PR6303 India
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
DepositionApr 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 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

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Assembly

Deposited unit
B: Aminoacyl-tRNA synthetase-interacting multifunctional protein p43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9293
Polymers21,8111
Non-polymers1182
Water00
1
B: Aminoacyl-tRNA synthetase-interacting multifunctional protein p43
hetero molecules

B: Aminoacyl-tRNA synthetase-interacting multifunctional protein p43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8586
Polymers43,6232
Non-polymers2364
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2210 Å2
ΔGint-54 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.396, 87.396, 53.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Aminoacyl-tRNA synthetase-interacting multifunctional protein p43 / Methionine-tRNA ligase / tRNA import protein tRIP


Mass: 21811.281 Da / Num. of mol.: 1 / 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) / References: UniProt: A0A1G4HHT8, UniProt: A0A0J9VJU0*PLUS
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2M sodium bromide, 5% ethyl acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.59 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.59 Å / Relative weight: 1
ReflectionResolution: 2.59→61.8 Å / Num. obs: 6539 / % possible obs: 95.8 % / Redundancy: 58.1 % / CC1/2: 1 / Rrim(I) all: 0.081 / Net I/σ(I): 27.1
Reflection shellResolution: 2.59→2.63 Å / Redundancy: 28.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 241 / CC1/2: 0.7 / Rrim(I) all: 3.353 / % possible all: 71.8

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.65 / FOM acentric: 0.64 / FOM centric: 0.66 / Reflection: 6429 / Reflection acentric: 5225 / Reflection centric: 1204
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.4-61.80.910.930.89337183154
4.6-7.40.840.860.76937681256
3.7-4.60.830.850.771137899238
3.2-3.70.720.740.621128929199
2.8-3.20.480.480.4619491668281
2.6-2.80.40.410.3694186576

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Processing

Software
NameVersionClassification
GDAdata collection
DIALSdata reduction
SOLVEphasing
RESOLVE2.15phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.59→61.8 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.958 / SU B: 43.464 / SU ML: 0.365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.983 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2742 305 4.7 %RANDOM
Rwork0.2197 ---
obs0.2222 6118 94.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 215.14 Å2 / Biso mean: 114.55 Å2 / Biso min: 64.54 Å2
Baniso -1Baniso -2Baniso -3
1-4.86 Å2-0 Å2-0 Å2
2--4.86 Å2-0 Å2
3----9.72 Å2
Refinement stepCycle: final / Resolution: 2.59→61.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 2 0 1383
Biso mean--104.82 --
Num. residues----167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191431
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9681926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2775165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.84424.70668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.81415275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.094154
X-RAY DIFFRACTIONr_chiral_restr0.1210.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021042
LS refinement shellResolution: 2.59→2.66 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 19 -
Rwork0.45 37 -
all-309 -
obs--69.9 %
Refinement TLS params.Method: refined / Origin x: 18.564 Å / Origin y: 27.139 Å / Origin z: 12.174 Å
111213212223313233
T0.0742 Å20.0555 Å2-0.0674 Å2-0.159 Å20.0201 Å2--0.2291 Å2
L6.4757 °22.3084 °2-2.4548 °2-5.4845 °2-1.4954 °2--9.3318 °2
S-0.1263 Å °0.5364 Å °0.4479 Å °-0.0809 Å °0.1037 Å °0.2529 Å °-0.6701 Å °-0.9022 Å °0.0226 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2 - 173
2X-RAY DIFFRACTION1B201 - 202

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