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- PDB-6jl3: Crystal Structure of the UBL domain of Plasmodium Falciparum Dsk2 -

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Basic information

Entry
Database: PDB / ID: 6jl3
TitleCrystal Structure of the UBL domain of Plasmodium Falciparum Dsk2
ComponentsUbiquitin domain-containing protein DSK2,putative
KeywordsSIGNALING PROTEIN / Ubiquitin binding / shuttle factor / ubiquitin
Function / homology
Function and homology information


Cargo recognition for clathrin-mediated endocytosis / polyubiquitin modification-dependent protein binding / ubiquitin-dependent protein catabolic process / mitochondrion / cytosol
Similarity search - Function
UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. ...UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin domain-containing protein DSK2, putative
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.303 Å
AuthorsGupta, I. / Khan, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (India)SP/YSP/136/2016-1063, India
CitationJournal: Mol.Biochem.Parasitol. / Year: 2020
Title: The recognition of proteasomal receptors by Plasmodium falciparum DSK2.
Authors: Gupta, I. / Khan, S.
History
DepositionMar 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 4, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 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: Ubiquitin domain-containing protein DSK2,putative


Theoretical massNumber of molelcules
Total (without water)8,6721
Polymers8,6721
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4420 Å2
Unit cell
Length a, b, c (Å)70.927, 70.927, 28.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-153-

HOH

21A-169-

HOH

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Components

#1: Protein Ubiquitin domain-containing protein DSK2,putative


Mass: 8672.269 Da / Num. of mol.: 1 / Fragment: UNP residues 1-77
Source method: isolated from a genetically manipulated source
Details: The initial two amino acid (MA) and the last three amino acid (AMA) electron density were missing.
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PF3D7_1113400 / Plasmid: pETM11 / Details (production host): His-tag / Cell line (production host): DE3 / Production host: Escherichia coli B83 (bacteria) / Strain (production host): B83 / References: UniProt: Q8IIM8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 39.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Bis-Tris pH 6.5 , 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 8, 2018 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.303→35.463 Å / Num. obs: 18008 / % possible obs: 99.45 % / Redundancy: 8.1 % / Biso Wilson estimate: 13.48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.016 / Rrim(I) all: 0.047 / Net I/σ(I): 24.47
Reflection shell

Diffraction-ID: 1 / Resolution: 1.303→1.35 Å

Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
7.30.637970.9830.2460.6395.89
6.90.02814610.0110.03199.46

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHENIXmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BWF

2bwf


Resolution: 1.303→35.46 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.36
RfactorNum. reflection% reflection
Rfree0.1677 1800 10 %
Rwork0.1558 --
obs0.1569 17995 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.2 Å2 / Biso mean: 16.9766 Å2 / Biso min: 8.79 Å2
Refinement stepCycle: final / Resolution: 1.303→35.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms573 0 0 83 656
Biso mean---28.01 -
Num. residues----74
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3033-1.33850.296132118395
1.3385-1.37790.21371331198100
1.3779-1.42240.21171361227100
1.4224-1.47320.15421371231100
1.4732-1.53220.14031360.12661223100
1.5322-1.6020.14681360.12451229100
1.602-1.68640.13131380.12921237100
1.6864-1.79210.14291391244100
1.7921-1.93040.13161380.13131251100
1.9304-2.12470.14841401252100
2.1247-2.43210.1451401266100
2.4321-3.06390.17741431288100
3.06390.19791521366100

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