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Open data
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Basic information
Entry | Database: PDB / ID: 2lyn | ||||||
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Title | HIGH RESOLUTION STRUCTURE OF RED ABALONE LYSIN DIMER | ||||||
![]() | SPERM LYSIN | ||||||
![]() | CELL ADHESION / ABALONE LYSIN / FERTILIZATION PROTEIN / GAMETE RECOGNITION PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kresge, N. / Vacquier, V.D. / Stout, C.D. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.4 KB | Display | ![]() |
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PDB format | ![]() | 97.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2lisC ![]() 1lynS 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16295.218 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 53.88 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 Details: 0.75 M (NH4)2SO4, 20 MM NH4SCN, 52.5 MM SODIUM-CITRATE-BORIC ACID BUFFER PH 4.5, 0.1 MM EDTA, 0.02% OTGP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / pH: 5.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→40.5 Å / Num. obs: 44137 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rsym value: 0.087 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.07→2.18 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.256 / % possible all: 94.6 |
Reflection | *PLUS Redundancy: 6.9 % / Num. measured all: 948262 / Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS % possible obs: 94.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.256 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LYN Resolution: 2.07→100 Å / Num. parameters: 18473 / Num. restraintsaints: 17746 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4604 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→100 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40.5 Å / Rfactor Rfree: 0.285 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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