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Yorodumi- PDB-7nqr: Plasmodium falciparum Hsp70-x chaperone nucleotide binding domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nqr | |||||||||
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Title | Plasmodium falciparum Hsp70-x chaperone nucleotide binding domain in complex with Z287256168 | |||||||||
Components | Heat shock protein 70 | |||||||||
Keywords | CHAPERONE / Intra-erythrocytic / AMP-PNP / Ligand | |||||||||
Function / homology | Function and homology information Regulation of HSF1-mediated heat shock response / AUF1 (hnRNP D0) binds and destabilizes mRNA / 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 ...Regulation of HSF1-mediated heat shock response / AUF1 (hnRNP D0) binds and destabilizes mRNA / 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 / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | |||||||||
Authors | Mohamad, N. / O'Donoghue, A. / Kantsadi, A.L. / Vakonakis, I. | |||||||||
Funding support | United Kingdom, European Union, 2items
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Citation | Journal: To Be Published Title: Structures of P. falciparum Hsp70-x nucleotide binding domain with small molecule ligands Authors: Mohamad, N. / O'Donoghue, A. / Kantsadi, A.L. / Vakonakis, I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nqr.cif.gz | 326.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nqr.ent.gz | 266.2 KB | Display | PDB format |
PDBx/mmJSON format | 7nqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nqr_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7nqr_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7nqr_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 7nqr_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/7nqr ftp://data.pdbj.org/pub/pdb/validation_reports/nq/7nqr | HTTPS FTP |
-Related structure data
Related structure data | 7nqsC 7nquC 7nqzC 7ooeC 6rzqS S: Starting model for refinement C: citing same article (ref.) |
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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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42828.441 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_0831700 / Plasmid: pFLOAT Details (production host): pET30a derivative, N-terminal His6-tag and HRC 3C cleavage site Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K7NTP5 |
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-Non-polymers , 7 types, 239 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PG6 / | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-SYQ / ( | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.48 Å3/Da / Density % sol: 50.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 20 mM HEPES pH 7.4 50 mM NaCl 1 mM DTT 3.5 mM AMP-PNP 24% w/v PEG 1500 20% v/v glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→63.33 Å / Num. obs: 42882 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 1 / Rrim(I) all: 0.09 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.22→2.26 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2097 / CC1/2: 0.6 / Rrim(I) all: 1.931 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RZQ Resolution: 2.22→63.33 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.278 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.283 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.195
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Displacement parameters | Biso mean: 85 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→63.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.24 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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