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- PDB-1tc6: Ligand Induced Conformational Shift in the N-terminal Domain of G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tc6 | ||||||
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Title | Ligand Induced Conformational Shift in the N-terminal Domain of GRP94, Open Conformation ADP-Complex | ||||||
![]() | Endoplasmin | ||||||
![]() | CHAPERONE / GRP94 / Hsp90 / ADP / Bergerat / Endoplasmic Reticulum | ||||||
Function / homology | ![]() Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / unfolded protein binding / melanosome ...Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / unfolded protein binding / melanosome / protein folding / response to heat / DNA damage response / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gewirth, D.T. / Immormino, R.M. / Dollins, D.E. / Shaffer, P.L. / Walker, M.A. / Soldano, K.L. | ||||||
![]() | ![]() Title: Ligand-induced Conformational Shift in the N-terminal Domain of GRP94, an Hsp90 Chaperone. Authors: Immormino, R.M. / Dollins, D.E. / Shaffer, P.L. / Soldano, K.L. / Walker, M.A. / Gewirth, D.T. | ||||||
History |
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Remark 600 | HETEROGEN ONLY FRAGMENTS OF PEG400 (PG4) WERE IDENTIFIED AND IN MANY CASES SEVERAL ATOMS WERE ...HETEROGEN ONLY FRAGMENTS OF PEG400 (PG4) WERE IDENTIFIED AND IN MANY CASES SEVERAL ATOMS WERE MISSING DUE TO LACK OF ELECTRON DENSITY. | ||||||
Remark 999 | SEQUENCE SEQUENCE DATABASE RESIDUES 287-327 WERE DELETED AND REPLACED BY 4 GLYCINES. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.4 KB | Display | ![]() |
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PDB format | ![]() | 79.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26514.012 Da / Num. of mol.: 2 Fragment: N-terminal Domain of GRP94 Residues (69-337), 287-327 deleted and replaced with 4 glycines Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG400, MgCl, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 2, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→50 Å / Num. obs: 43460 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 28.7 Å2 / Rsym value: 0.06 / Net I/σ(I): 49.6 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4310 / Rsym value: 0.01 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.3262 Å2 / ksol: 0.351169 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.87→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.99 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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