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- PDB-5zkh: Crystal Structure of N-terminal Domain of Plasmodium falciparum p43 -

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Basic information

Entry
Database: PDB / ID: 5zkh
TitleCrystal Structure of N-terminal Domain of Plasmodium falciparum p43
ComponentsAminoacyl tRNA synthetase complex-interacting multifunctional protein P43
KeywordsLIGASE / GST-like domain / AIMP1 / Plasmodium
Function / homology
Function and homology information


: / : / 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
tRNA-binding domain-containing protein
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.991 Å
AuthorsManickam, Y. / Sharma, A. / Khan, S.
CitationJournal: To Be Published
Title: Structural analysis of aminoacyl-tRNA synthetase-interacting multifunctional proteins from plasmodium species
Authors: Manickam, Y. / Sharma, A.
History
DepositionMar 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 complex-interacting multifunctional protein P43
B: Aminoacyl tRNA synthetase complex-interacting multifunctional protein P43


Theoretical massNumber of molelcules
Total (without water)42,7942
Polymers42,7942
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-13 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.710, 44.371, 77.472
Angle α, β, γ (deg.)90.000, 111.940, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Aminoacyl tRNA synthetase complex-interacting multifunctional protein P43


Mass: 21396.859 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate Dd2) (eukaryote)
Gene: PFDG_03875 / Plasmid: pETM-11 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0L7M8L6

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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: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350

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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: Feb 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7156 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.081 / Χ2: 1.348 / Net I/σ(I): 10.5 / Num. measured all: 43159
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3-3.055.30.5523371.455198.8
3.05-3.115.50.513621.363199.7
3.11-3.175.70.4643521.351199.4
3.17-3.235.80.4263481.334199.4
3.23-3.360.3813671.2681100
3.3-3.3860.2863351.312199.4
3.38-3.466.10.2313771.324199.7
3.46-3.566.30.1863261.2671100
3.56-3.666.20.163651.2441100
3.66-3.786.30.1443621.3021100
3.78-3.916.20.1133581.3371100
3.91-4.076.30.0933521.3651100
4.07-4.266.20.083551.3371100
4.26-4.486.30.0633601.3931100
4.48-4.766.20.0613521.3481100
4.76-5.136.20.0543581.3571100
5.13-5.646.20.0633741.3981100
5.64-6.466.10.0613611.2811100
6.46-8.136.10.0443641.3191100
8.13-505.70.0313911.6171100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.991→36.464 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 335 4.69 %
Rwork0.2142 --
obs0.2161 7144 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.46 Å2 / Biso mean: 72.5903 Å2 / Biso min: 32.48 Å2
Refinement stepCycle: final / Resolution: 2.991→36.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 0 0 2499
Num. residues----328
Refinement TLS params.Method: refined / Origin x: -9.5789 Å / Origin y: 3.7971 Å / Origin z: 17.2137 Å
111213212223313233
T0.4723 Å2-0.0116 Å20.0216 Å2-0.3832 Å2-0.0362 Å2--0.3779 Å2
L3.5341 °20.7848 °2-0.6255 °2-2.4033 °2-0.1102 °2--2.1418 °2
S0.0025 Å °0.007 Å °-0.0754 Å °0.0836 Å °-0.0036 Å °0.2449 Å °-0.0512 Å °-0.0276 Å °0.0428 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 171
2X-RAY DIFFRACTION1allB2 - 171

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