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- PDB-2arr: Human plasminogen activator inhibitor-2.[loop (66-98) deletion mu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2arr | ||||||
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Title | Human plasminogen activator inhibitor-2.[loop (66-98) deletion mutant] complexed with peptide n-acetyl-teaaagmggvmtgr-oh | ||||||
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![]() | hydrolase inhibitor/peptide / SERPIN / PEPTIDE BINDING / inhibitor / hydrolase inhibitor-peptide complex | ||||||
Function / homology | ![]() cornified envelope / Dissolution of Fibrin Clot / fibrinolysis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / serine-type endopeptidase inhibitor activity / negative regulation of apoptotic process / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Di Giusto, D.A. / Sutherland, A.P. / Jankova, L. / Harrop, S.J. / Curmi, P.M. / King, G.C. | ||||||
![]() | ![]() Title: Plasminogen activator inhibitor-2 is highly tolerant to P8 residue substitution--implications for serpin mechanistic model and prediction of nsSNP activities Authors: Di Giusto, D.A. / Sutherland, A.P. / Jankova, L. / Harrop, S.J. / Curmi, P.M. / King, G.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.1 KB | Display | ![]() |
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PDB format | ![]() | 72.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.2 KB | Display | ![]() |
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Full document | ![]() | 437.8 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 28.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2arqC ![]() 1jrrS S: Starting model for refinement C: citing same article ( |
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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: 42986.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1335.531 Da / Num. of mol.: 1 / Mutation: T8M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: peg 8K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2000 / Details: MONOCHROMATOR |
Radiation | Monochromator: yes / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→33.7 Å / Num. all: 56875 / Num. obs: 56875 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 22.9 Å2 / Rsym value: 0.055 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 7024 / Rsym value: 0.392 / % possible all: 84.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JRR Resolution: 1.55→30.7 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.582 / SU ML: 0.058 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.085 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.148 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→30.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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