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Open data
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Basic information
Entry | Database: PDB / ID: 1fiw | |||||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF BETA-ACROSIN FROM RAM SPERMATOZOA | |||||||||
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![]() | HYDROLASE / anti-parallel beta-barrel | |||||||||
Function / homology | ![]() acrosin / acrosome reaction / fucose binding / amidase activity / D-mannose binding / single fertilization / activation of adenylate cyclase activity / serine-type peptidase activity / acrosomal vesicle / serine-type endopeptidase activity / proteolysis Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Tranter, R. / Read, J.A. / Jones, R. / Brady, R.L. | |||||||||
![]() | ![]() Title: Effector sites in the three-dimensional structure of mammalian sperm beta-acrosin. Authors: Tranter, R. / Read, J.A. / Jones, R. / Brady, R.L. #1: ![]() Title: Three Dimensional Structure of Acrosin from Ram and Boar Spermatozoa Authors: Tranter, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.2 KB | Display | ![]() |
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PDB format | ![]() | 55 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 810.1 KB | Display | ![]() |
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Full document | ![]() | 820.1 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | Heterodimer of chain A and L linked together by two disulphide bonds |
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Components
#1: Protein | Mass: 32002.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
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#2: Protein/peptide | Mass: 2440.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
#3: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.15 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: sodium acetate, sodium formate, p-aminobenzamidine, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.2 / 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: Oct 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 23810 / Num. obs: 20601 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.298 / Num. unique all: 2710 / % possible all: 92.9 |
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Processing
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Refinement | Resolution: 2.1→30 Å / SU B: 5.61319 / SU ML: 0.14893 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.20194 / ESU R Free: 0.18313 / Stereochemistry target values: Engh and Huber / Details: Maximum likelihood refinement
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Displacement parameters | Biso mean: 37.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5.2 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |