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- PDB-5ii8: Orthorhombic crystal structure of red abalone lysin at 0.99 A res... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ii8 | |||||||||||||||||||||
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Title | Orthorhombic crystal structure of red abalone lysin at 0.99 A resolution | |||||||||||||||||||||
![]() | Egg-lysin | |||||||||||||||||||||
![]() | CELL ADHESION / FERTILIZATION / EGG-SPERM INTERACTION / GAMETE RECOGNITION / EGG-BINDING PROTEIN / ACROSOMAL PROTEIN / EGG COAT PENETRATION / CRYSTAL DEHYDRATION | |||||||||||||||||||||
Function / homology | ![]() | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Sadat Al-Hosseini, H. / Raj, I. / Nishimura, K. / De Sanctis, D. / Jovine, L. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of Egg Coat-Sperm Recognition at Fertilization. Authors: Raj, I. / Sadat Al Hosseini, H. / Dioguardi, E. / Nishimura, K. / Han, L. / Villa, A. / de Sanctis, D. / Jovine, L. #1: ![]() Title: 1.35 and 2.07 A resolution structures of the red abalone sperm lysin monomer and dimer reveal features involved in receptor binding. Authors: Kresge, N. / Vacquier, V.D. / Stout, C.D. #2: ![]() Title: Crystal structure and subunit dynamics of the abalone sperm lysin dimer: egg envelopes dissociate dimers, the monomer is the active species. Authors: Shaw, A. / Fortes, P.A. / Stout, C.D. / Vacquier, V.D. #3: ![]() Title: The crystal structure of lysin, a fertilization protein. Authors: Shaw, A. / McRee, D.E. / Vacquier, V.D. / Stout, C.D. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111 KB | Display | ![]() |
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PDB format | ![]() | 88.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.3 KB | Display | ![]() |
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Full document | ![]() | 443 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ii4C ![]() 5ii5C ![]() 5ii6C ![]() 5ii7SC ![]() 5ii9C ![]() 5iiaC ![]() 5iibC ![]() 5iicC ![]() 5mr2C ![]() 5mr3C 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: 16483.465 Da / Num. of mol.: 1 / Fragment: UNP residues 19-154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MES / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.65 M ammonium sulfate, 0.2 M NaCl, 0.1 M CHES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 0.99→39.422 Å / Num. obs: 101171 / % possible obs: 94.12 % / Redundancy: 4.89 % / Biso Wilson estimate: 11.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 0.99→1.01 Å / Redundancy: 4.86 % / Rmerge(I) obs: 2.006 / Mean I/σ(I) obs: 1.1 / % possible all: 87.44 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5II7 Resolution: 0.99→39.422 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.99→39.422 Å
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Refine LS restraints |
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LS refinement shell |
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