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Yorodumi- PDB-6zhi: Structure of the Plasmodium falciparum Hsp70-x substrate binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zhi | ||||||
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Title | Structure of the Plasmodium falciparum Hsp70-x substrate binding domain in complex with hydrophobic peptide | ||||||
Components |
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Keywords | CHAPERONE / malaria / erythrocyte remodelling / PfHsp70-x / complex | ||||||
Function / homology | Function and homology information Regulation of HSF1-mediated heat shock response / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / chaperone cofactor-dependent protein refolding / protein folding chaperone / heat shock protein binding / ATP-dependent protein folding chaperone / protein refolding / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Schmidt, J. / Vakonakis, I. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acta Crystallographica Section F Title: Structure of the PfHsp70-x SBD Authors: Schmidt, J. / Vakonakis, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zhi.cif.gz | 269.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zhi.ent.gz | 213.1 KB | Display | PDB format |
PDBx/mmJSON format | 6zhi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/6zhi ftp://data.pdbj.org/pub/pdb/validation_reports/zh/6zhi | HTTPS FTP |
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-Related structure data
Related structure data | 4po2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 25835.967 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Gene: PF3D7_0831700 / Plasmid: pFLOAT Details (production host): pET30a derivative with His-tag and 3C cleavage site Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: K7NTP5 #2: Protein/peptide | Mass: 786.941 Da / Num. of mol.: 4 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M bicine/2-Amino-2-(hydroxymethyl)propane-1,3-diol base 10% w/v PEG 20,000 20% w/v PEG MME 550 0.03 M of each of di- to penta-ethyleneglycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→93.89 Å / Num. obs: 17457 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 94.35 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.048 / Rrim(I) all: 0.125 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.25→3.31 Å / Redundancy: 1.5 % / Rmerge(I) obs: 1.857 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 796 / CC1/2: 0.568 / Rpim(I) all: 0.777 / Rrim(I) all: 2.016 / % possible all: 94.09 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PO2 Resolution: 3.25→84.13 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.885 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.635
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Displacement parameters | Biso mean: 152.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.81 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.25→84.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.25→3.28 Å / Total num. of bins used: 42
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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