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Yorodumi- PDB-1y6z: Middle domain of Plasmodium falciparum putative heat shock protei... -
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-Basic information
Entry | Database: PDB / ID: 1y6z | ||||||
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Title | Middle domain of Plasmodium falciparum putative heat shock protein PF14_0417 | ||||||
Components | heat shock protein, putativeHeat shock response | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / heat shock / chaperone / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information 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 / response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity ...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 / response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å | ||||||
Authors | Lunin, V.V. / Botchkareva, E. / Loppnau, P. / Amani, M. / Bray, J. / Vedadi, M. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Bochkarev, A. ...Lunin, V.V. / Botchkareva, E. / Loppnau, P. / Amani, M. / Bray, J. / Vedadi, M. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Plotnikova, O. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Mol.Biochem.Parasitol. / Year: 2007 Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms. Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y6z.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y6z.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 1y6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/1y6z ftp://data.pdbj.org/pub/pdb/validation_reports/y6/1y6z | HTTPS FTP |
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-Related structure data
Related structure data | 1txjC 1xccC 1z6gC 1z7dC 1z81C 1zo2C 2a22C 2a4aC 2aifC 2amxC 2aqwC 2av4C 2awpC 2ayvC 2b71C 2bddC 2f4zC 2fdsC 2ffcC 2fo3C 2fu0C 2ghiC 2h1rC 2h2yC 2h66C 2hjrC 2hteC 2hvgC 3pggC 3tb2C 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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Unit cell |
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-Components
#1: Protein | Mass: 30564.783 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Plasmid: pet11-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IL32 #2: 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: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: PEG3350, TRIS-HCl, NaCl, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 28, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→59 Å / Num. all: 39020 / Num. obs: 38123 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.88→58.93 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.317 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.349 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→58.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.876→1.925 Å / Total num. of bins used: 20
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