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- PDB-1qlp: 2.0 ANGSTROM STRUCTURE OF INTACT ALPHA-1-ANTITRYPSIN: A CANONICAL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qlp | |||||||||
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Title | 2.0 ANGSTROM STRUCTURE OF INTACT ALPHA-1-ANTITRYPSIN: A CANONICAL TEMPLATE FOR ACTIVE SERPINS | |||||||||
![]() | ALPHA-1-ANTITRYPSIN | |||||||||
![]() | SERINE PROTEASE INHIBITOR / SERPIN / GLYCOPROTEIN / POLYMORPHISM / EMPHYSEMA / DISEASE MUTATION / ACUTE PHASE | |||||||||
Function / homology | ![]() Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation ...Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / protease binding / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Elliott, P.R. / Pei, X.Y. / Dafforn, T. / Read, R.J. / Carrell, R.W. / Lomas, D.A. | |||||||||
![]() | ![]() Title: Topography of a 2.0 A structure of alpha1-antitrypsin reveals targets for rational drug design to prevent conformational disease. Authors: Elliott, P.R. / Pei, X.Y. / Dafforn, T.R. / Lomas, D.A. #1: Journal: J.Mol.Biol. / Year: 1998 Title: Wildtype Alpha1-Antitrypsin is in the Canonical Inhibitory Conformation Authors: Elliott, P.R. / Abrahams, J.-P. / Lomas, D.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.3 KB | Display | ![]() |
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PDB format | ![]() | 66.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.4 KB | Display | ![]() |
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Full document | ![]() | 436 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1psiS 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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Unit cell |
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Components
#1: Protein | Mass: 44380.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 37.2 % Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD. | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 24% PEG 4000, 0.2 M SODIUM ACETATE, 0.1M TRIS-HCL PH 6.0, 2MM FESO4.7H20 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 9, 1998 / Details: MIRRORS |
Radiation | Monochromator: BENT CYLINDRICAL GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 25057 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 29.41 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.067 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.415 / % possible all: 95.2 |
Reflection | *PLUS Num. measured all: 156306 |
Reflection shell | *PLUS Redundancy: 2.2 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 1.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: THERMOSTABLE VARIANT ALPHA1-ANTITRYPSIN (PDB ENTRY 1PSI) Resolution: 2→25 Å / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R-VALUE / σ(F): 0 Details: THE N-TERMINAL RESIDUES 1-22 WERE NOT OBSERVED IN THE ELECTRON DENSITY MAPS
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Solvent computation | Solvent model: CNS / Bsol: 215 Å2 / ksol: 1.257 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.38 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Total num. of bins used: 10
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Xplor file |
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Refine LS restraints | *PLUS
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