[English] 日本語
Yorodumi- PDB-1fiz: THREE DIMENSIONAL STRUCTURE OF BETA-ACROSIN FROM BOAR SPERMATOZOA -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fiz | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | THREE DIMENSIONAL STRUCTURE OF BETA-ACROSIN FROM BOAR SPERMATOZOA | |||||||||
Components | (BETA-ACROSIN ...) x 2 | |||||||||
Keywords | HYDROLASE / anti-parallel beta-barrel | |||||||||
Function / homology | Function and homology information acrosin / acrosomal matrix / acrosome reaction / fucose binding / amidase activity / D-mannose binding / single fertilization / activation of adenylate cyclase activity / serine-type peptidase activity / serine-type endopeptidase activity ...acrosin / acrosomal matrix / acrosome reaction / fucose binding / amidase activity / D-mannose binding / single fertilization / activation of adenylate cyclase activity / serine-type peptidase activity / serine-type endopeptidase activity / protein-containing complex / proteolysis Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å | |||||||||
Authors | Tranter, R. / Read, J.A. / Jones, R. / Brady, R.L. | |||||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 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: Journal: Thesis Title: Three dimensional structure of beta-acrosin from ram and boar spermatozoa Authors: Tranter, R. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fiz.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fiz.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fiz_validation.pdf.gz | 812.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1fiz_full_validation.pdf.gz | 823.9 KB | Display | |
Data in XML | 1fiz_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 1fiz_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/1fiz ftp://data.pdbj.org/pub/pdb/validation_reports/fi/1fiz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | heterodimer of chain A and B linked together by two disulphide bonds |
-Components
-BETA-ACROSIN ... , 2 types, 2 molecules AL
#1: Protein | Mass: 29229.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Cell: SPERMATOZOA / Organ: TESTIS / References: UniProt: P08001 |
---|---|
#2: Protein/peptide | Mass: 2615.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Cell: SPERMATOZOA / Organ: TESTIS / References: UniProt: P08001 |
-Sugars , 1 types, 1 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 3 types, 30 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-PBZ / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, ammonium sulphate, sodium cacodylate, p-aminobenzamidine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.2 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.244 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.244 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→100 Å / Num. all: 8303 / Num. obs: 8303 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 65.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.9→3.1 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.307 / Num. unique all: 1200 / % possible all: 99.8 |
Reflection | *PLUS Num. obs: 8711 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.9→30 Å / SU B: 18.1713 / SU ML: 0.34735 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.41073 Details: maximun likelihood refinement CNS was also used for refinement.
| ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.027 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 4.7 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |