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- PDB-1ojm: SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ojm | |||||||||
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Title | SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE: COMPLEX WITH UNSULPHATED CHONDROITIN DISACCHARIDE | |||||||||
![]() | HYALURONATE LYASE | |||||||||
![]() | LYASE / PROTEIN-CARBOHYDRATE COMPLEX | |||||||||
Function / homology | ![]() hyaluronate lyase / hyaluronate lyase activity / : / hydrolase activity, acting on glycosyl bonds / carbohydrate binding / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rigden, D.J. / Jedrzejas, M.J. | |||||||||
![]() | ![]() Title: Structures of Streptococcus Pneumoniae Hyaluronate Lyase in Complex with Chondroitin and Chondroitin Sulfate Disaccharides: Insights Into Specificity and Mechanism of Action Authors: Rigden, D.J. / Jedrzejas, M.J. #1: ![]() Title: Structural Basis of Hyaluronan Degradation by Streptococcus Pneumoniae Hyaluronate Lyase Authors: Li, S. / Kelly, S.J. / Lamani, E. / Ferraroni, M. / Jedrzejas, M.J. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.5 KB | Display | ![]() |
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PDB format | ![]() | 134.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 819.4 KB | Display | ![]() |
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Full document | ![]() | 841.2 KB | Display | |
Data in XML | ![]() | 35.1 KB | Display | |
Data in CIF | ![]() | 51.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ojnC ![]() 1ojoC ![]() 1ojpC ![]() 1c82S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 83403.781 Da / Num. of mol.: 1 / Fragment: HYALURONATE LYASE, RESIDUES 287-1009 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Polysaccharide | 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose / UNSATURATED CHONDROITIN DISACCHARIDE | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | THE SIX RESIDUE HIS TAG (RESIDUES A893-A898) WAS NOT SEEN IN THE DENSITY. THE SWISSPROT ENTRY ...THE SIX RESIDUE HIS TAG (RESIDUES A893-A898) WAS NOT SEEN IN THE DENSITY. THE SWISSPROT ENTRY INCLUDES REFERENCES | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.6 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 3.5M AMMONIUM SULFATE, 200MM SODIUM CACODYLATE, PH 6.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
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: OXFORD / Detector: CCD / Date: Jun 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→40.38 Å / Num. obs: 70193 / % possible obs: 84.2 % / Redundancy: 2.5 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.78→1.84 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 4.6 / % possible all: 76.5 |
Reflection | *PLUS Highest resolution: 1.78 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 76.5 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 4.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1C82 Resolution: 1.78→40.38 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2193081 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.1651 Å2 / ksol: 0.413387 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.78→40.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.84 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Num. reflection obs: 72283 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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