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Yorodumi- PDB-4xcl: N-terminal domain of Hsp90 from Dictyostelium discoideum in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xcl | ||||||
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Title | N-terminal domain of Hsp90 from Dictyostelium discoideum in complex with AGS | ||||||
Components | Heat shock cognate 90 kDa protein | ||||||
Keywords | CHAPERONE / Hsp90 / AGS | ||||||
Function / homology | Function and homology information regulation of aggregation involved in sorocarp development / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Regulation of actin dynamics for phagocytic cup formation / eNOS activation / HSF1 activation / HSF1-dependent transactivation / Sema3A PAK dependent Axon repulsion / VEGFR2 mediated vascular permeability / The NLRP3 inflammasome / Aryl hydrocarbon receptor signalling ...regulation of aggregation involved in sorocarp development / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Regulation of actin dynamics for phagocytic cup formation / eNOS activation / HSF1 activation / HSF1-dependent transactivation / Sema3A PAK dependent Axon repulsion / VEGFR2 mediated vascular permeability / The NLRP3 inflammasome / Aryl hydrocarbon receptor signalling / Extra-nuclear estrogen signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Neutrophil degranulation / phagocytic vesicle / extracellular matrix / ATP-dependent protein folding chaperone / unfolded protein binding / protein stabilization / ATP hydrolysis activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å | ||||||
Authors | Raman, S. / Suguna, K. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: First Structural View of a Peptide Interacting with the Nucleotide Binding Domain of Heat Shock Protein 90 Authors: Raman, S. / Singh, M. / Tatu, U. / Suguna, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xcl.cif.gz | 119 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xcl.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xcl_validation.pdf.gz | 781.6 KB | Display | wwPDB validaton report |
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Full document | 4xcl_full_validation.pdf.gz | 782.4 KB | Display | |
Data in XML | 4xcl_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 4xcl_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/4xcl ftp://data.pdbj.org/pub/pdb/validation_reports/xc/4xcl | HTTPS FTP |
-Related structure data
Related structure data | 4xc0C 4xcjSC 4xd8C 4xdmC 4xe2C 4xkaC 4xkoC C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 29226.871 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-223 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Strain: AX2 / Gene: hspD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta / References: UniProt: P54651 |
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#2: Chemical | ChemComp-AGS / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.5 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes, PEG 3350 / PH range: 7.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 4, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→56.94 Å / Num. obs: 64120 / % possible obs: 95.7 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.21→1.28 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 5.2 / % possible all: 92.5 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XCJ Resolution: 1.21→56.94 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.11 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.042 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.067 Å2
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Refinement step | Cycle: LAST / Resolution: 1.21→56.94 Å
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