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Yorodumi- PDB-1hm2: ACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hm2 | |||||||||
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Title | ACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE OF ENZYME-OLIGOSACCHARIDE COMPLEXES AND MUTAGENESIS | |||||||||
Components | CHONDROITINASE AC | |||||||||
Keywords | LYASE / protein-oligosaccharide complex / active site / catalysis | |||||||||
Function / homology | Function and homology information chondroitin AC lyase / chondroitin AC lyase activity / carbohydrate binding / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Pedobacter heparinus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | |||||||||
Authors | Huang, W. / Boju, L. / Tkalec, L. / Su, H. / Yang, H.O. / Gunay, N.S. / Linhardt, R.J. / Kim, Y.S. / Matte, A. / Cygler, M. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis. Authors: Huang, W. / Boju, L. / Tkalec, L. / Su, H. / Yang, H.O. / Gunay, N.S. / Linhardt, R.J. / Kim, Y.S. / Matte, A. / Cygler, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hm2.cif.gz | 152.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hm2.ent.gz | 120.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hm2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/1hm2 ftp://data.pdbj.org/pub/pdb/validation_reports/hm/1hm2 | 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 79797.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pedobacter heparinus (bacteria) / Production host: Pedobacter heparinus (bacteria) / References: UniProt: Q59288, chondroitin AC lyase |
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-Sugars , 3 types, 3 molecules
#2: Polysaccharide | 2-O-methyl-beta-L-fucopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)- ...2-O-methyl-beta-L-fucopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | alpha-L-idopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-alpha- ...alpha-L-idopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 2 types, 314 molecules
#5: Chemical | ChemComp-CA / |
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#6: 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: 2.27 Å3/Da / Density % sol: 45.91 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, sodium acetate, hepes , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 1999 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 48610 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2→2.2 Å / Rmerge(I) obs: 0.244 / % possible all: 87.2 |
Reflection | *PLUS Num. measured all: 204934 |
Reflection shell | *PLUS % possible obs: 87.6 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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