+Open data
-Basic information
Entry | Database: PDB / ID: 4xbi | ||||||
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Title | Structure Of A Malarial Protein Involved in Proteostasis | ||||||
Components | ClpB protein, putative,Green fluorescent protein | ||||||
Keywords | CHAPERONE / CLP Chaperone / AAA+ ATPase / Refoldase / Protein Metabolism | ||||||
Function / homology | Function and homology information apicoplast / protein unfolding / bioluminescence / generation of precursor metabolites and energy / cellular response to heat / protein refolding / mitochondrial matrix / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.013 Å | ||||||
Authors | Egea, P.F. / Ah Young, A.P. / Cascio, D. | ||||||
Citation | Journal: Protein Sci. / Year: 2015 Title: Structural mapping of the ClpB ATPases of Plasmodium falciparum: Targeting protein folding and secretion for antimalarial drug design. Authors: AhYoung, A.P. / Koehl, A. / Cascio, D. / Egea, P.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xbi.cif.gz | 310.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xbi.ent.gz | 252.2 KB | Display | PDB format |
PDBx/mmJSON format | 4xbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xbi_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 4xbi_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 4xbi_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 4xbi_validation.cif.gz | 45.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/4xbi ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xbi | HTTPS FTP |
-Related structure data
Related structure data | 4iodSC 4irfSC 2b3pS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43281.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote), (gene. exp.) Aequorea victoria (jellyfish) Strain: isolate 3D7 / Gene: PF08_0063, GFP / Plasmid: pRSF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q8IB03, UniProt: P42212 #2: Chemical | ChemComp-SO4 / #3: 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: 2.51 Å3/Da / Density % sol: 51.03 % / Description: bright yellow hexagonal shaped |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 2 M ammonium sulphate 100 mM Hepes pH=7 protein at 13-15 mg/ml PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→70.946 Å / Num. all: 55948 / Num. obs: 55948 / % possible obs: 98.6 % / Redundancy: 5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.94 |
Reflection shell | Resolution: 2.01→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.68 / % possible all: 90.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B3P, 4IOD and 4IRF Resolution: 2.013→70.946 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.013→70.946 Å
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Refine LS restraints |
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LS refinement shell |
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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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