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- PDB-6rzy: Plasmodium falciparum PFA0660w Hsp40 co-chaperone J-domain -

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Basic information

Entry
Database: PDB / ID: 6rzy
TitlePlasmodium falciparum PFA0660w Hsp40 co-chaperone J-domain
ComponentsHeat shock protein 40, type IIHeat shock response
KeywordsCHAPERONE / Malaria Exported co-chaperone Intra-erythrocytic
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / MAPK6/MAPK4 signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / host cell cytosol / chaperone cofactor-dependent protein refolding / unfolded protein binding / response to heat / protein-folding chaperone binding / membrane => GO:0016020 / cytosol
Similarity search - Function
HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain
Similarity search - Domain/homology
Heat shock protein 40, type II
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.379 Å
AuthorsVakonakis, I. / Day, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Medical Research Council (United Kingdom)MR/N009274/1 United Kingdom
CitationJournal: Faseb J. / Year: 2019
Title: ThePlasmodium falciparumHsp70-x chaperone assists the heat stress response of the malaria parasite.
Authors: Day, J. / Passecker, A. / Beck, H.P. / Vakonakis, I.
History
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 11, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein 40, type II
B: Heat shock protein 40, type II


Theoretical massNumber of molelcules
Total (without water)16,3112
Polymers16,3112
Non-polymers00
Water2,234124
1
A: Heat shock protein 40, type II


Theoretical massNumber of molelcules
Total (without water)8,1551
Polymers8,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock protein 40, type II


Theoretical massNumber of molelcules
Total (without water)8,1551
Polymers8,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.828, 54.925, 51.441
Angle α, β, γ (deg.)90.00, 98.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heat shock protein 40, type II / Heat shock response


Mass: 8155.302 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_0113700 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8I2E1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12 M mix of ethylene glycols 0.1 M Tris (base)/Bicine 30% w/v PEG MME550 30% w/v PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.0389 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0389 Å / Relative weight: 1
ReflectionResolution: 1.379→54.925 Å / Num. obs: 28692 / % possible obs: 97.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 12.73 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.046 / Rrim(I) all: 0.086 / Net I/σ(I): 9.5
Reflection shellResolution: 1.379→1.403 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1444 / CC1/2: 0.495 / Rpim(I) all: 0.427 / Rrim(I) all: 0.772 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RWU

4rwu


Resolution: 1.379→37.338 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.75
RfactorNum. reflection% reflection
Rfree0.2027 1335 4.66 %
Rwork0.1647 --
obs0.1665 28661 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.379→37.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1140 0 0 124 1264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081162
X-RAY DIFFRACTIONf_angle_d1.0271556
X-RAY DIFFRACTIONf_dihedral_angle_d11.095450
X-RAY DIFFRACTIONf_chiral_restr0.06160
X-RAY DIFFRACTIONf_plane_restr0.006198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.379-1.42830.32351360.28872774X-RAY DIFFRACTION99
1.4283-1.48550.31400.24122753X-RAY DIFFRACTION100
1.4855-1.55310.2551330.19232798X-RAY DIFFRACTION100
1.5531-1.6350.20021410.15262771X-RAY DIFFRACTION100
1.635-1.73740.24061140.13772820X-RAY DIFFRACTION100
1.7374-1.87160.17471310.13782779X-RAY DIFFRACTION100
1.8716-2.05990.18361200.13572692X-RAY DIFFRACTION99
2.0599-2.3580.18271300.13992408X-RAY DIFFRACTION90
2.358-2.97060.20741450.16722767X-RAY DIFFRACTION99
2.9706-37.35160.18311450.16632764X-RAY DIFFRACTION97

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