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- PDB-7qrn: Crystal structure of Ovalbumin-related protein X (OVAX) complexed... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qrn | ||||||
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Title | Crystal structure of Ovalbumin-related protein X (OVAX) complexed with fondaparinux | ||||||
![]() | Ovalbumin-related protein X | ||||||
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Function / homology | ![]() serine-type endopeptidase inhibitor activity / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Coste, F. / Bruneau, G. / Rehault-Godbert, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Antimicrobial Proteins and Peptides in Avian Eggshell: Structural Diversity and Potential Roles in Biomineralization. Authors: Moreau, T. / Gautron, J. / Hincke, M.T. / Monget, P. / Rehault-Godbert, S. / Guyot, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166 KB | Display | ![]() |
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PDB format | ![]() | 127.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ovaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 45481.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
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#2: Polysaccharide | 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside / ![]() | ||||||
#3: Chemical | ChemComp-SO4 / ![]() #4: Chemical | ChemComp-EDO / ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.36 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: phosphate/citrate, LiSO4, PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.83→57.66 Å / Num. obs: 35271 / % possible obs: 99.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 32.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.02 / Rrim(I) all: 0.048 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.832→1.863 Å / Redundancy: 5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1691 / CC1/2: 0.801 / Rpim(I) all: 0.385 / Rrim(I) all: 0.883 / % possible all: 97.9 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1OVA Resolution: 1.83→38.09 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.46 Å2 / Biso mean: 44.9539 Å2 / Biso min: 19.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.83→38.09 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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