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Yorodumi- PDB-1fcv: CRYSTAL STRUCTURE OF BEE VENOM HYALURONIDASE IN COMPLEX WITH HYAL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fcv | |||||||||
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Title | CRYSTAL STRUCTURE OF BEE VENOM HYALURONIDASE IN COMPLEX WITH HYALURONIC ACID TETRAMER | |||||||||
Components | HYALURONOGLUCOSAMINIDASEHyaluronidase | |||||||||
Keywords | HYDROLASE / 7 stranded TIM barrel / allergen / glycosidase family 56 / hyaluronic acid | |||||||||
Function / homology | Function and homology information hyaluronoglucosaminidase / hyalurononglucosaminidase activity / defense response / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Apis mellifera (honey bee) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.65 Å | |||||||||
Authors | Markovic-Housley, Z. / Miglierini, G. / Soldatova, L. / Rizkallah, P.J. / Mueller, U. / Schirmer, T. | |||||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Crystal structure of hyaluronidase, a major allergen of bee venom. Authors: Markovic-Housley, Z. / Miglierini, G. / Soldatova, L. / Rizkallah, P.J. / Muller, U. / Schirmer, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fcv.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fcv.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/1fcv ftp://data.pdbj.org/pub/pdb/validation_reports/fc/1fcv | HTTPS FTP |
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-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: 40901.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Apis mellifera (honey bee) / Cell (production host): HIGH-FIVE INSECT CELLS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q08169, hyaluronoglucosaminidase |
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#2: Polysaccharide | alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid Source method: isolated from a genetically manipulated source |
#3: 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: 2.7 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, ammonium sulphate, Na acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.4 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→30 Å / Num. all: 13411 / Num. obs: 13411 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.295 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 99.9 % / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Resolution: 2.65→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.65→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.18 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |