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Yorodumi- PDB-1u2o: Crystal Structure Of The N-Domain Of Grp94 Lacking The Charged Do... -
+Open data
-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 | |||||||||
Components | Endoplasmin | |||||||||
Keywords | CHAPERONE / GRP94 / Hsp90 / Bergerat / Endoplasmic reticulum / NECA | |||||||||
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 / : / ATP-dependent protein folding chaperone / melanosome / unfolded protein binding ...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 / : / ATP-dependent protein folding chaperone / melanosome / unfolded protein binding / protein folding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Canis lupus familiaris (dog) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Soldano, K.L. / Jivan, A. / Nicchitta, C.V. / Gewirth, D.T. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u2o.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u2o.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 1u2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/1u2o ftp://data.pdbj.org/pub/pdb/validation_reports/u2/1u2o | HTTPS FTP |
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-Related structure data
Related structure data | 1qy8C 1qyeC 6d28C 1qy5 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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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.) 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 | ChemComp-PG4 / #4: Chemical | ChemComp-1PE / | #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: 2.44 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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