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- PDB-1u2o: Crystal Structure Of The N-Domain Of Grp94 Lacking The Charged Do... -
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Basic information
Entry | Database: PDB / ID: 1u2o | |||||||||
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Title | Crystal Structure Of The N-Domain Of Grp94 Lacking The Charged Domain In Complex With Neca | |||||||||
![]() | Endoplasmin | |||||||||
![]() | CHAPERONE / GRP94 / Hsp90 / Bergerat / Endoplasmic reticulum / NECA | |||||||||
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 | ![]() ![]() | |||||||||
![]() | Soldano, K.L. / Jivan, A. / Nicchitta, C.V. / Gewirth, D.T. | |||||||||
![]() | ![]() Title: Structure of the N-terminal domain of GRP94. Basis for ligand specificity and regulation Authors: Soldano, K.L. / Jivan, A. / Nicchitta, C.V. / Gewirth, D.T. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.8 KB | Display | ![]() |
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PDB format | ![]() | 86.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 995.9 KB | Display | ![]() |
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Full document | ![]() | 1009.7 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qy8C ![]() 1qyeC ![]() 6d28C ![]() 1qy5 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26514.012 Da / Num. of mol.: 2 / Fragment: N-terminal Domain of GRP94 Residues (69-337) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PG4 / #4: Chemical | ChemComp-1PE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: PEG 400, MAGNESIUM CHLORIDE, TRIS, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 9, 2002 / Details: YALE MIRRORS |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 27334 / % possible obs: 87.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.049 / Net I/σ(I): 40.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 4.54 / Rsym value: 0.238 / % possible all: 50.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QY5 ![]() 1qy5 Resolution: 2.1→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 478653.72 / 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: 64.0263 Å2 / ksol: 0.34489 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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