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Yorodumi- PDB-1tc6: Ligand Induced Conformational Shift in the N-terminal Domain of G... -
+Open data
-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 | ||||||
Components | Endoplasmin | ||||||
Keywords | CHAPERONE / GRP94 / Hsp90 / ADP / Bergerat / Endoplasmic Reticulum | ||||||
Function / homology | Function and homology information 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 | Canis lupus familiaris (dog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Gewirth, D.T. / Immormino, R.M. / Dollins, D.E. / Shaffer, P.L. / Walker, M.A. / Soldano, K.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tc6.cif.gz | 106.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tc6.ent.gz | 79.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tc6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1tc6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1tc6_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 1tc6_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/1tc6 ftp://data.pdbj.org/pub/pdb/validation_reports/tc/1tc6 | HTTPS FTP |
-Related structure data
-Links
-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.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: TRA1 / Plasmid: PGEX-NB-GRP94 (69-337delta41) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41148 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 212341.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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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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