+Open data
-Basic information
Entry | Database: PDB / ID: 1cb8 | |||||||||
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Title | CHONDROITINASE AC LYASE FROM FLAVOBACTERIUM HEPARINUM | |||||||||
Components | PROTEIN (CHONDROITINASE AC) | |||||||||
Keywords | LYASE / CHONDROITIN DEGRADATION | |||||||||
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 / MIRAS / Resolution: 1.9 Å | |||||||||
Authors | Fethiere, J. / Eggimann, B. / Cygler, M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structure of chondroitin AC lyase, a representative of a family of glycosaminoglycan degrading enzymes. Authors: Fethiere, J. / Eggimann, B. / Cygler, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and preliminary analysis of chondroitinase AC from Flavobacterium heparinum. Authors: Fethiere, J. / Shilton, B.H. / Li, Y. / Allaire, M. / Laliberte, M. / Eggimann, B. / Cygler, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cb8.cif.gz | 165.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cb8.ent.gz | 124.3 KB | Display | PDB format |
PDBx/mmJSON format | 1cb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/1cb8 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/1cb8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 77358.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pedobacter heparinus (bacteria) / Cellular location: INTRACELLULARGlossary of biology / References: UniProt: Q59288, chondroitin AC lyase |
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#2: Polysaccharide | methyl alpha-L-fucopyranoside-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)- ...methyl alpha-L-fucopyranoside-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose Type: oligosaccharide / Mass: 794.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Sequence details | PDB SEGMENT NUMBERED ACCORDING TO PRECURSOR SEQUENCE. THE FIRST THREE N-TERMINAL RESIDUES, AND THE ...PDB SEGMENT NUMBERED ACCORDING TO PRECURSOR SEQUENCE. THE FIRST THREE N-TERMINAL RESIDUES, AND THE C-TERMINAL RESIDUE WERE NOT VISIBLE IN ELECTRON DENSITY MAPS, AND THEREFORE WERE NOT INCLUDED IN THE MODEL. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % / Description: MIRAS COMPLEMENTED BY MAD | ||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: CRYSTALLIZATION CONDITIONS: PEG-MME 2K 17% AMMONIUM ACETATE 80MM PH 6.5 0.4M SODIUM ACETATE | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
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: CHESS / Beamline: F1 / Wavelength: 0.908 |
Detector | Type: ADSC / Detector: CCD / Date: Oct 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 60889 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 5.5 / Rsym value: 0.212 / % possible all: 34.7 |
Reflection shell | *PLUS % possible obs: 78.8 % / Rmerge(I) obs: 0.175 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.9→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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Displacement parameters | Biso mean: 30.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.01 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å / Rfactor obs: 0.196 / Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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