+Open data
-Basic information
Entry | Database: PDB / ID: 1oo8 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF A1PI-PITTSBURGH IN THE NATIVE CONFORMATION | ||||||
Components | Alpha-1-antitrypsin precursor | ||||||
Keywords | HYDROLASE INHIBITOR / SERPIN / PITTSBURGH VARIANT | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Dementiev, A. / Simonovic, M. / Volz, K. / Gettins, P.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Canonical inhibitor-like interactions explain reactivity of alpha1-proteinase inhibitor Pittsburgh and antithrombin with proteinases Authors: Dementiev, A. / Simonovic, M. / Volz, K. / Gettins, P.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1oo8.cif.gz | 88 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1oo8.ent.gz | 66.2 KB | Display | PDB format |
PDBx/mmJSON format | 1oo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/1oo8 ftp://data.pdbj.org/pub/pdb/validation_reports/oo/1oo8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ophC 1qlpS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 44276.258 Da / Num. of mol.: 1 / Fragment: RESIDUES 26-418 Mutation: F51L, T59A, T68A, A70G, C232S, M358R, M374I, S381A, K387R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: HEPATOCYTES / Cell: NEUTROPHILS / Cellular location: CYTOPLASM / Gene: SERPINA1 OR PI OR AAT / Organ: LIVER / Plasmid: PQE30 / Cell line (production host): SG13900 / Gene (production host): ALPHA-1-ANTITRYPSIN / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P01009 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.06 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.2M TRI-POTASSIUM CITRATE, 20% PEG-3350, pH 6.30, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 6, 2001 / Details: FOCUSING MIRRORS |
Radiation | Monochromator: NI FILTER + MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→40 Å / Num. all: 12840 / Num. obs: 12840 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.88 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.65→2.74 Å / Redundancy: 4.12 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.7 / % possible all: 93.6 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 103240 |
Reflection shell | *PLUS % possible obs: 93.6 % / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QLP Resolution: 2.65→34.25 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.9132 Å2 / ksol: 0.263093 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→34.25 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.65→2.82 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|