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Yorodumi- PDB-3ina: Crystal structure of heparin lyase I H151A mutant complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ina | |||||||||
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Title | Crystal structure of heparin lyase I H151A mutant complexed with a dodecasaccharide heparin | |||||||||
Components | Heparin lyase I | |||||||||
Keywords | LYASE / jelly roll | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Han, Y.H. / Ryu, K.S. / Kim, H.Y. / Jeon, Y.H. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural snapshots of heparin depolymerization by heparin lyase I Authors: Han, Y.H. / Garron, M.L. / Kim, H.Y. / Kim, W.S. / Zhang, Z. / Ryu, K.S. / Shaya, D. / Xiao, Z. / Cheong, C. / Kim, Y.S. / Linhardt, R.J. / Jeon, Y.H. / Cygler, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ina.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ina.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ina.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ina_validation.pdf.gz | 830.7 KB | Display | wwPDB validaton report |
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Full document | 3ina_full_validation.pdf.gz | 837.3 KB | Display | |
Data in XML | 3ina_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 3ina_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/3ina ftp://data.pdbj.org/pub/pdb/validation_reports/in/3ina | HTTPS FTP |
-Related structure data
Related structure data | 3ikwC 3ilrC 3imnSC 3in9C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 42767.297 Da / Num. of mol.: 1 / Mutation: H151A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: WAL2926 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89YQ6*PLUS | ||
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#2: Polysaccharide | 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-CA / | ||
#4: Water | ChemComp-HOH / | ||
Nonpolymer details | SGN, IDS AND NGN FORMS DODECASACCSequence details | THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. ALA 151 WAS ...THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.02 % / Mosaicity: 0.524 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10% glycerol, 8% PEG 1500, Sarcosine, vapor diffusion, hanging drop, temperature 293K, pH 5.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 9, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 33588 / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.067 / Χ2: 1.91 / Net I/σ(I): 18.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IMN Resolution: 1.9→36.82 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso max: 91.84 Å2 / Biso mean: 30.996 Å2 / Biso min: 14.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→36.82 Å
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Refine LS restraints |
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Xplor file |
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