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Open data
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Basic information
Entry | Database: PDB / ID: 1psi | ||||||
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Title | Intact recombined alpha1-antitrypsin mutant PHE 51 to LEU | ||||||
![]() | 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 | ![]() ![]() | ||||||
![]() | Abrahams, J.P. / Elliott, P.R. / Lomas, D.A. / Carrell, R.W. | ||||||
![]() | ![]() Title: Inhibitory conformation of the reactive loop of alpha 1-antitrypsin. Authors: Elliott, P.R. / Lomas, D.A. / Carrell, R.W. / Abrahams, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81 KB | Display | ![]() |
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PDB format | ![]() | 63.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418 KB | Display | ![]() |
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Full document | ![]() | 430.4 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9apiS 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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Unit cell |
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Components
#1: Protein | Mass: 44406.539 Da / Num. of mol.: 1 / Mutation: F51L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 24% PEG, 0.2 M SODIUM ACETATE, 0.1 M TRIS.HCL, PH 6.0, 0.002 M FESO4, 25 DEG CELSIUS | |||||||||||||||||||||||||||||||||||
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: IMAGE PLATE / Date: Feb 12, 1996 / Details: NICKEL COATED DOUBLE MIRROR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→19.5 Å / Num. obs: 7651 / % possible obs: 91.7 % / Observed criterion σ(I): 3.5 / Redundancy: 2.2 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 8.36 |
Reflection shell | Resolution: 2.91→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 4 / Rsym value: 0.204 / % possible all: 74.4 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 6 Å / Rmerge(I) obs: 0.114 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 3.1 Å / % possible obs: 74.4 % / Rmerge(I) obs: 0.204 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: CLEAVED ALPHA1-ANTITRYPSIN (PDB ENTRY 9API) Resolution: 2.92→6 Å / σ(F): 0 Details: RESIDUES 106 - 108 ARE POORLY ORDERED. ALTHOUGH SOME CONNECTED DENSITY EXISTS, A STEREOCHEMICALLY CORRECT MODEL FITTING THE DATA COULD NOT BE BUILT. THE OCCUPANCIES OF THESE RESIDUES ARE SET ...Details: RESIDUES 106 - 108 ARE POORLY ORDERED. ALTHOUGH SOME CONNECTED DENSITY EXISTS, A STEREOCHEMICALLY CORRECT MODEL FITTING THE DATA COULD NOT BE BUILT. THE OCCUPANCIES OF THESE RESIDUES ARE SET TO ZERO. PRO 106 - SER 108 IS A POORLY ORDERED LOOP, PRESENT IN MULTIPLE CONFORMATIONS. A STEREOCHEMICALLY VALID MODEL WAS BUILT, BUT THE OCCUPANCIES ARE SET TO ZERO.
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Refinement step | Cycle: LAST / Resolution: 2.92→6 Å
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Refine LS restraints |
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Software | *PLUS Name: 'TNT and X-PLOR' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.218 / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.215 / Highest resolution: 2.9 Å / Num. reflection all: 6699 / Num. reflection Rfree: 754 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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