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Yorodumi- PDB-4xdm: N-terminal domain of Hsp90 from Dictyostelium discoideum in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xdm | ||||||
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Title | N-terminal domain of Hsp90 from Dictyostelium discoideum in complex with Geldanamycin | ||||||
Components | Heat shock cognate 90 kDa protein | ||||||
Keywords | CHAPERONE / Hsp90 / Geldanamycin | ||||||
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: 1.5 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 | 4xdm.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xdm.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/4xdm ftp://data.pdbj.org/pub/pdb/validation_reports/xd/4xdm | HTTPS FTP |
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-Related structure data
Related structure data | 4xc0C 4xcjSC 4xclC 4xd8C 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-GDM / |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å |
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 |
-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: 1.5→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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