+Open data
-Basic information
Entry | Database: PDB / ID: 1gak | ||||||
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Title | CRYSTAL STRUCTURE OF GREEN ABALONE SP18 | ||||||
Components | FERTILIZATION PROTEIN | ||||||
Keywords | CELL ADHESION / helical bundle | ||||||
Function / homology | Fertilization protein / Egg lysin (Sperm-lysin) / Egg-lysin superfamily / Egg lysin (Sperm-lysin) / Lysin / single fertilization / Up-down Bundle / Mainly Alpha / Egg-lysin Function and homology information | ||||||
Biological species | Haliotis fulgens (green abalone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.85 Å | ||||||
Authors | Kresge, N. / Vacquier, V.D. / Stout, C.D. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: The crystal structure of a fusagenic sperm protein reveals extreme surface properties. 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 | 1gak.cif.gz | 42.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gak.ent.gz | 30.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gak_validation.pdf.gz | 424.6 KB | Display | wwPDB validaton report |
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Full document | 1gak_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 1gak_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 1gak_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/1gak ftp://data.pdbj.org/pub/pdb/validation_reports/ga/1gak | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16954.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haliotis fulgens (green abalone) / Cell: SPERM / References: UniProt: Q25063 |
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#2: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.85 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3 Details: mPEG 5000, Ammonium Acetate, Sodium Phosphate, pH 3, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 4.9 | ||||||||||||||||||||||||||||||
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: 0.77 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 14, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.77 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→59.76 Å / Num. all: 15134 / Num. obs: 15134 / % possible obs: 98.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 29.35 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.4 / % possible all: 98.9 |
Reflection | *PLUS Num. measured all: 82274 |
Reflection shell | *PLUS % possible obs: 98.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.85→60 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.5 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→60 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 60 Å / σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor obs: 0.227 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.5 Å2 |