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Yorodumi- PDB-1ofm: CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO CHONDROITIN 4-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ofm | |||||||||||||||
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Title | CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO CHONDROITIN 4-SULFATE TETRASACCHARIDE | |||||||||||||||
Components | CHONDROITINASE B | |||||||||||||||
Keywords | LYASE / ACTIVE SITE / BETA-ELIMINATION / CHONDROITIN 4-SULFATE | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | PEDOBACTER HEPARINUS (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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. / 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 | 1ofm.cif.gz | 137.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ofm.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 1ofm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/1ofm ftp://data.pdbj.org/pub/pdb/validation_reports/of/1ofm | HTTPS FTP |
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-Related structure data
Related structure data | 1oflC 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
#1: Protein | Mass: 53688.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: HYDROXY-PROLINE AT 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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#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 |
#3: Polysaccharide | 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D- ...4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
#4: 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: 1.8→33.18 Å / Num. obs: 40172 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.75 % / Biso Wilson estimate: 6.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.085 / Mean I/σ(I) obs: 9.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DBG Resolution: 1.8→33.18 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1399907.18 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.4551 Å2 / ksol: 0.309859 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→33.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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