[English] 日本語
Yorodumi- PDB-3opd: Crystal Structure of the N-terminal domain of an HSP90 from Trypa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3opd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the N-terminal domain of an HSP90 from Trypanosoma Brucei, Tb10.26.1080 in the presence of a benzamide derivative | ||||||
Components | Heat shock protein 83Heat shock response | ||||||
Keywords | CHAPERONE / Structural Genomics / Structural Genomics Consortium / SGC / ATP binding | ||||||
Function / homology | Function and homology information response to unfolded protein / unfolded protein binding / protein folding / response to heat / protein refolding / centrosome / ATP hydrolysis activity / nucleoplasm / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Pizarro, J.C. / Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / Chamberlain, K. / Weadge, J. / Cossar, D. / Li, Y. / Kozieradzki, I. / Bochkarev, A. ...Pizarro, J.C. / Wernimont, A.K. / Hutchinson, A. / Sullivan, H. / Chamberlain, K. / Weadge, J. / Cossar, D. / Li, Y. / Kozieradzki, I. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Wyatt, P.G. / Fairlamb, A.H. / MacKenzie, C. / Ferguson, M.A.J. / Hui, R. / Hills, T. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: PLoS Negl Trop Dis / Year: 2013 Title: Exploring the Trypanosoma brucei Hsp83 potential as a target for structure guided drug design. Authors: Pizarro, J.C. / Hills, T. / Senisterra, G. / Wernimont, A.K. / Mackenzie, C. / Norcross, N.R. / Ferguson, M.A. / Wyatt, P.G. / Gilbert, I.H. / Hui, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3opd.cif.gz | 258.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3opd.ent.gz | 207.7 KB | Display | PDB format |
PDBx/mmJSON format | 3opd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/3opd ftp://data.pdbj.org/pub/pdb/validation_reports/op/3opd | HTTPS FTP |
---|
-Related structure data
Related structure data | 3o6oC 3omuC 3u67C 3h80S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26200.381 Da / Num. of mol.: 3 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HSP83, Tb10.26.1080 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12861 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.29 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.0 M AMMONIUM SULFATE 2% PEG400 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
---|---|
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 24, 2010 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→29.6 Å / Num. obs: 24726 / % possible obs: 99.7 % / Biso Wilson estimate: 60.61 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.0678 / Net I/σ(I): 112.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3H80 Resolution: 2.6→29.85 Å / Cor.coef. Fo:Fc: 0.9341 / Cor.coef. Fo:Fc free: 0.9056 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.35 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.345 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→29.85 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.71 Å / Total num. of bins used: 12
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|