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Yorodumi- PDB-1lxm: Crystal Structure of Streptococcus agalactiae Hyaluronate Lyase C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lxm | |||||||||
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Title | Crystal Structure of Streptococcus agalactiae Hyaluronate Lyase Complexed with Hexasaccharide Unit of Hyaluronan | |||||||||
Components | HYALURONATE Lyase | |||||||||
Keywords | LYASE / Streptococcus agalactiae / Protein-carbohydrate complex / hyaluronan | |||||||||
Function / homology | Function and homology information hyaluronate lyase / hyaluronate lyase activity / organic substance catabolic process / carbohydrate binding / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Streptococcus agalactiae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Mello, L.V. / de Groot, B.L. / Li, S. / Jedrzejas, M.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structure and flexibility of Streptococcus agalactiae hyaluronate lyase complex with its substrate. Insights into the mechanism of processive degradation of hyaluronan. Authors: Mello, L.V. / De Groot, B.L. / Li, S. / Jedrzejas, M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lxm.cif.gz | 180.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lxm.ent.gz | 138.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/1lxm ftp://data.pdbj.org/pub/pdb/validation_reports/lx/1lxm | HTTPS FTP |
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-Related structure data
Related structure data | 1f1sS 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: 92510.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae (bacteria) / Gene: hyl / Production host: Escherichia coli (E. coli) References: UniProt: q53591, UniProt: Q53591*PLUS, hyaluronate lyase |
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#2: Polysaccharide | beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose 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: 2.55 Å3/Da / Density % sol: 51.75 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 5500 MME, KSCN, CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 Details: Jedrzejas, M.J., (2000) Acta Crystallogr., Sect.D, 56, 460. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→50 Å / Num. all: 45372 / Num. obs: 45372 / % possible obs: 93.7 % / Redundancy: 5.5 % / Rsym value: 0.144 | |||||||||||||||
Reflection shell | Resolution: 2.2→2.28 Å / Rsym value: 0.921 / % possible all: 71.4 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 233927 / Rmerge(I) obs: 0.144 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 71.4 % / Rmerge(I) obs: 0.921 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1f1s Resolution: 2.2→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 2.5 % | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / Rfactor Rfree: 0.367 / Rfactor Rwork: 0.326 |