+Open data
-Basic information
Entry | Database: PDB / ID: 2lis | ||||||
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Title | HIGH RESOLUTION STRUCTURE OF THE RED ABALONE LYSIN MONOMER | ||||||
Components | SPERM LYSIN | ||||||
Keywords | CELL ADHESION / ABALONE LYSIN / FERTILIZATION PROTEIN / GAMETE RECOGNITION PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Haliotis rufescens (red abalone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.35 Å | ||||||
Authors | Kresge, N. / Vacquier, V.D. / Stout, C.D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lis.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lis.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 2lis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lis_validation.pdf.gz | 408.5 KB | Display | wwPDB validaton report |
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Full document | 2lis_full_validation.pdf.gz | 410.5 KB | Display | |
Data in XML | 2lis_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 2lis_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/2lis ftp://data.pdbj.org/pub/pdb/validation_reports/li/2lis | HTTPS FTP |
-Related 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: 16295.218 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haliotis rufescens (red abalone) / Cell: SPERM / Organ: GONAD / Organelle: ACROSOME GRANULE / References: UniProt: P04552 |
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#2: 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: 2.9 Å3/Da / Density % sol: 57.3 % Description: STRUCTURE WAS REFINED BY PHASE EXTENSION USING 1.9 A STRUCTURE OF RED ABALONE LYSIN MONOMER AS A STARTING POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9.5 Details: 1.26 M AMMONIUM SULFATE, 100 MM CHESS PH 9.5, 200 MM NACL, pH 9.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
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: 1.35→18.6 Å / Num. obs: 41576 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rsym value: 4.5 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.35→1.38 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 8.6 / Rsym value: 8.2 / % possible all: 88.7 |
Reflection | *PLUS Highest resolution: 1.35 Å / Lowest resolution: 18.6 Å / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Num. measured all: 259591 / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS Highest resolution: 1.35 Å / Lowest resolution: 1.38 Å / % possible obs: 88.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 8.6 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.35→100 Å / Num. parameters: 12587 / Num. restraintsaints: 14715 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 1133 / Occupancy sum non hydrogen: 1388 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→100 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.35 Å / Lowest resolution: 100 Å / Rfactor Rwork: 0.136 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 14.7 Å2 |