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- PDB-4ro9: 2.0A resolution structure of SRPN2 (S358E) from Anopheles gambiae -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ro9 | ||||||
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Title | 2.0A resolution structure of SRPN2 (S358E) from Anopheles gambiae | ||||||
![]() | Serpin 2 | ||||||
![]() | Hydrolase Inhibitor / serpin / serine protease inhibitor / insect immunity | ||||||
Function / homology | ![]() negative regulation of melanization defense response / negative regulation of endopeptidase activity / negative regulation of protein processing / defense response to protozoan / negative regulation of proteolysis / serine-type endopeptidase inhibitor activity / innate immune response / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lovell, S. / Battaile, K.P. / Zhang, X. / Meekins, D.A. / An, C. / Michel, K. | ||||||
![]() | ![]() Title: Structural and Inhibitory Effects of Hinge Loop Mutagenesis in Serpin-2 from the Malaria Vector Anopheles gambiae. Authors: Zhang, X. / Meekins, D.A. / An, C. / Zolkiewski, M. / Battaile, K.P. / Kanost, M.R. / Lovell, S. / Michel, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 222.6 KB | Display | ![]() |
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PDB format | ![]() | 177.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.8 KB | Display | ![]() |
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Full document | ![]() | 465.2 KB | Display | |
Data in XML | ![]() | 38.9 KB | Display | |
Data in CIF | ![]() | 54.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4roaC ![]() 4rsqC ![]() 3pzfS C: citing same article ( 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | There are 3 biological units in the asymmetric unit. |
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Components
#1: Protein | Mass: 45405.629 Da / Num. of mol.: 3 / Mutation: S358E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SRPN2 / Plasmid: pET28a / Production host: ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.07 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 20% (w/v) PEG 3350, 100mM Bis-Tris Propane, 200 mM Sodium Malonate, pH 8.5, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2012 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2→93.15 Å / Num. obs: 80845 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 32.17 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.8 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3PZF Resolution: 2→38.183 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 25.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.51 Å2 / Biso mean: 41.1477 Å2 / Biso min: 18.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→38.183 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29
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