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Yorodumi- PDB-5umb: Crystal structure of ATPase domain of Malaria GRP78 with ADP bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 5umb | ||||||
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Title | Crystal structure of ATPase domain of Malaria GRP78 with ADP bound | ||||||
Components | Chaperone DnaK | ||||||
Keywords | CHAPERONE / ATPase domain | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium falciparum NF54 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Chen, Y. / Antoshchenko, T. / Pizarro, J.C. / Song, J.H. / Park, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2018 Title: Repurposing drugs to target the malaria parasite unfolding protein response. Authors: Chen, Y. / Murillo-Solano, C. / Kirkpatrick, M.G. / Antoshchenko, T. / Park, H.W. / Pizarro, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5umb.cif.gz | 597.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5umb.ent.gz | 492.1 KB | Display | PDB format |
PDBx/mmJSON format | 5umb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/5umb ftp://data.pdbj.org/pub/pdb/validation_reports/um/5umb | HTTPS FTP |
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-Related structure data
Related structure data | 5f1xS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 42046.844 Da / Num. of mol.: 4 / Fragment: UNP residues 10-387 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum NF54 (eukaryote) / Strain: isolate NF54 / Gene: PFNF54_05546 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W7JXN5 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-ADP / #5: Water | ChemComp-HOH / | |
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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: 2.54 Å3/Da / Density % sol: 51.54 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 30% PEG 8K, 0.2M NH4SO4, 0.1M Na CaCo, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2016 |
Radiation | Monochromator: Double Crystal Monochromator (ACCEL DCM) with an indirectly cryo-cooled first crystal and sagittally focusing second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.08 Å / Num. obs: 76738 / % possible obs: 99.5 % / Redundancy: 3.38 % / Net I/av σ(I): 1.92 / Net I/σ(I): 7.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5f1x Resolution: 2.3→48.08 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.857 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.345 / SU Rfree Blow DPI: 0.24 / SU Rfree Cruickshank DPI: 0.246
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Displacement parameters | Biso max: 249.56 Å2 / Biso mean: 33.03 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→48.08 Å
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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