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Yorodumi- PDB-3eka: Crystal structure of the complex of hyaluranidase trimer with asc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eka | |||||||||
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Title | Crystal structure of the complex of hyaluranidase trimer with ascorbic acid at 3.1 A resolution reveals the locations of three binding sites | |||||||||
Components | Hyaluronidase, phage associated | |||||||||
Keywords | LYASE / ASCORBIC ACID COMPLEX / HYALURONAN LYASE / PHAGE TAIL FIBRE / TRIPLE-STRANDED | |||||||||
Function / homology | Hyaluronidase, bacterial / Hyaluronidase protein (HylP) / Major tropism determinant, N-terminal domain / Major tropism determinant N-terminal domain / hyalurononglucosaminidase activity / capsule polysaccharide biosynthetic process / ASCORBIC ACID / Hyaluronidase, phage associated Function and homology information | |||||||||
Biological species | Streptococcus pyogenes (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Mishra, P. / Ethayathulla, A.S. / Prem Kumar, R. / Singh, N. / Sharma, S. / Kaur, P. / Bhakuni, V. / Singh, T.P. | |||||||||
Citation | Journal: Febs J. / Year: 2009 Title: Polysaccharide binding sites in hyaluronate lyase--crystal structures of native phage-encoded hyaluronate lyase and its complexes with ascorbic acid and lactose. Authors: Mishra, P. / Prem Kumar, R. / Ethayathulla, A.S. / Singh, N. / Sharma, S. / Perbandt, M. / Betzel, C. / Kaur, P. / Srinivasan, A. / Bhakuni, V. / Singh, T.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eka.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eka.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 3eka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eka_validation.pdf.gz | 449.2 KB | Display | wwPDB validaton report |
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Full document | 3eka_full_validation.pdf.gz | 465.1 KB | Display | |
Data in XML | 3eka_validation.xml.gz | 17 KB | Display | |
Data in CIF | 3eka_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/3eka ftp://data.pdbj.org/pub/pdb/validation_reports/ek/3eka | HTTPS FTP |
-Related structure data
Related structure data | 2yw0C 2c3fS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35797.172 Da / Num. of mol.: 1 / Fragment: residues 7-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: hylP1, HYLP2, SPy_0701 / Plasmid: PET 21D / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A0M7, hyaluronate lyase | ||
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#2: Sugar | #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: 2.68 Å3/Da / Density % sol: 54.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: TRIS HCL, SODIUM FORMATE, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 203 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.803 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 10, 2007 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.803 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 6874 / Num. obs: 6874 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.11 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3.1→3.15 Å / Mean I/σ(I) obs: 2.67 / Rsym value: 0.434 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2C3F Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.878 / SU B: 20.1 / SU ML: 0.362 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.619 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.59 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.17 Å / Total num. of bins used: 20
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