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Yorodumi- PDB-3k60: Crystal structure of N-terminal domain of Plasmodium falciparum H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k60 | ||||||
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Title | Crystal structure of N-terminal domain of Plasmodium falciparum Hsp90 (PF07_0029) bound to ADP | ||||||
Components | Heat shock protein 86 | ||||||
Keywords | CHAPERONE / ATPase / Stress response | ||||||
Function / homology | Function and homology information Aryl hydrocarbon receptor signalling / eNOS activation / VEGFR2 mediated vascular permeability / Extra-nuclear estrogen signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding ...Aryl hydrocarbon receptor signalling / eNOS activation / VEGFR2 mediated vascular permeability / Extra-nuclear estrogen signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Corbett, K.D. / Berger, J.M. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Structure of the ATP-binding domain of Plasmodium falciparum Hsp90. Authors: Corbett, K.D. / Berger, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k60.cif.gz | 192.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k60.ent.gz | 153.3 KB | Display | PDB format |
PDBx/mmJSON format | 3k60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k60_validation.pdf.gz | 837.7 KB | Display | wwPDB validaton report |
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Full document | 3k60_full_validation.pdf.gz | 839.7 KB | Display | |
Data in XML | 3k60_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 3k60_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/3k60 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/3k60 | HTTPS FTP |
-Related structure data
Related structure data | 1yetS 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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Unit cell |
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-Components
#1: Protein | Mass: 25238.396 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: Deletion mutant Delta(212-301)/GGG Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: Hsp90 (PF07_0029), PF07_0029 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q8IC05 #2: Chemical | ChemComp-ADP / | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | RESIDUES 212-301 ARE REPLACED WITH "GGG" LINKER. | |
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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: 4.23 Å3/Da / Density % sol: 70.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.8-2.0 M Li2SO4, 0.1 M HEPES pH 7.5, 1-2% Xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2009 / Details: mirrors |
Radiation | Monochromator: side-bounce cryogenically-cooled Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 38117 / Num. obs: 38117 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 42.44 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3747 / Rsym value: 0.824 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YET Resolution: 2.3→34.1124 Å / SU ML: 0.28 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ML / Details: Two TLS groups: chain A, chain B
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.164 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.1 Å2
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Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→34.1124 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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