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Yorodumi- PDB-5ii8: Orthorhombic crystal structure of red abalone lysin at 0.99 A res... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ii8 | |||||||||||||||||||||
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Title | Orthorhombic crystal structure of red abalone lysin at 0.99 A resolution | |||||||||||||||||||||
Components | Egg-lysin | |||||||||||||||||||||
Keywords | CELL ADHESION / FERTILIZATION / EGG-SPERM INTERACTION / GAMETE RECOGNITION / EGG-BINDING PROTEIN / ACROSOMAL PROTEIN / EGG COAT PENETRATION / CRYSTAL DEHYDRATION | |||||||||||||||||||||
Function / homology | Function and homology information | |||||||||||||||||||||
Biological species | Haliotis rufescens (red abalone) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å | |||||||||||||||||||||
Authors | Sadat Al-Hosseini, H. / Raj, I. / Nishimura, K. / De Sanctis, D. / Jovine, L. | |||||||||||||||||||||
Funding support | Sweden, 6items
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Citation | Journal: Cell / Year: 2017 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: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2000 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: Journal: J. Cell Biol. / Year: 1995 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: Journal: Science / Year: 1993 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ii8.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ii8.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ii8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/5ii8 ftp://data.pdbj.org/pub/pdb/validation_reports/ii/5ii8 | HTTPS FTP |
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-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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Haliotis rufescens (red abalone) / Plasmid: pJexpress411 / Details (production host): DNA2.0 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRARE star / References: UniProt: P04552 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MES / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8856 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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