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Yorodumi- PDB-1ofl: CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ofl | ||||||||||||
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Title | CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFATE HEXASACCHARIDE | ||||||||||||
Components | CHONDROITINASE B | ||||||||||||
Keywords | LYASE / ACTIVE SITE / BETA-ELIMINATION / DEMATAN SULFATE | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | PEDOBACTER HEPARINUS (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Michel, G. / Cygler, M. | ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The Structure of Chondroitin B Lyase Complexed with Glycosaminoglycan Oligosaccharides Unravels a Calcium-Dependent Catalytic Machinery Authors: Michel, G. / Pojasek, K. / Li, Y. / Sulea, T. / Linhardt, R.J. / Raman, R. / Prabhakar, V. / Sasisekharan, R. / Cygler, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ofl.cif.gz | 137 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ofl.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ofl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/1ofl ftp://data.pdbj.org/pub/pdb/validation_reports/of/1ofl | HTTPS FTP |
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-Related structure data
Related structure data | 1ofmC 1dbgS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53688.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: HYDROXYPROLINE AT THE N-TERMINUS, GLYCOSYLATION AT SER234 Source: (gene. exp.) PEDOBACTER HEPARINUS (bacteria) / Production host: PEDOBACTER HEPARINUS (bacteria) / References: UniProt: Q46079, EC: 4.2.2.4 |
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-Sugars , 3 types, 5 molecules
#2: Polysaccharide | alpha-D-galactopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]2-O-methyl-alpha-L-fucopyranose-(1-4)- ...alpha-D-galactopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]2-O-methyl-alpha-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 | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-alpha-D-galactopyranose | Source method: isolated from a genetically manipulated source |
-Non-polymers , 2 types, 758 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: 1.95 Å3/Da / Density % sol: 34.9 % |
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Crystal grow | pH: 8.7 Details: PEG8000, 2-METHYL-2,4- PENTADIOL, AMMONIUM ACETATE, TRIS, pH 8.70 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→34.98 Å / Num. obs: 44254 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 2.85 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 5.5 / % possible all: 65.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DBG Resolution: 1.7→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.708 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.47 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refine LS restraints |
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