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- PDB-4xdm: N-terminal domain of Hsp90 from Dictyostelium discoideum in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xdm | ||||||
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Title | N-terminal domain of Hsp90 from Dictyostelium discoideum in complex with Geldanamycin | ||||||
![]() | Heat shock cognate 90 kDa protein | ||||||
![]() | CHAPERONE / Hsp90 / Geldanamycin | ||||||
Function / homology | ![]() 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 / disordered domain specific binding / 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Raman, S. / Suguna, K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.2 KB | Display | ![]() |
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PDB format | ![]() | 80.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 885.1 KB | Display | ![]() |
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Full document | ![]() | 886.5 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xc0C ![]() 4xcjSC ![]() 4xclC ![]() 4xd8C ![]() 4xe2C ![]() 4xkaC ![]() 4xkoC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GDM / |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.02 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Hepes, PEG 3350 / PH range: 7.0 - 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→57.24 Å / Num. obs: 33584 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
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Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 4XCJ Resolution: 1.5→57.24 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.317 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.084 / 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: 27.028 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→57.24 Å
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Refine LS restraints |
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