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Yorodumi- PDB-2wda: The X-ray structure of the Streptomyces coelicolor A3 Chondroitin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wda | |||||||||
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Title | The X-ray structure of the Streptomyces coelicolor A3 Chondroitin AC Lyase in Complex with Chondroitin sulphate | |||||||||
Components | PUTATIVE SECRETED LYASE | |||||||||
Keywords | LYASE / HYALURONATE LYASE / CHONDROITIN LYASE / FAMILY 8 | |||||||||
Function / homology | Function and homology information carbohydrate binding / carbohydrate metabolic process / lyase activity / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | STREPTOMYCES VIOLACEORUBER (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Elmabrouk, Z.H. / Taylor, E.J. / Vincent, F. / Smith, N.L. / Turkenburg, J.P. / Davies, G.J. / Black, G.W. | |||||||||
Citation | Journal: Proteins / Year: 2011 Title: Crystal Structures of a Family 8 Polysaccharide Lyase Reveal Open and Highly Occluded Substrate-Binding Cleft Conformations. Authors: Elmabrouk, Z.H. / Vincent, F. / Zhang, M. / Smith, N.L. / Turkenburg, J.P. / Charnock, S.J. / Black, G.W. / Taylor, E.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wda.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wda.ent.gz | 132.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wda_validation.pdf.gz | 950.9 KB | Display | wwPDB validaton report |
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Full document | 2wda_full_validation.pdf.gz | 967.7 KB | Display | |
Data in XML | 2wda_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 2wda_validation.cif.gz | 53.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/2wda ftp://data.pdbj.org/pub/pdb/validation_reports/wd/2wda | HTTPS FTP |
-Related structure data
Related structure data | 2wcoSC 2x03C 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 / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 83022.234 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-776 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES VIOLACEORUBER (bacteria) / Strain: A3(2) Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) DSM NO. 40783 Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O86516, hyaluronate lyase |
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#2: Polysaccharide | 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 517 molecules
#3: Chemical | ChemComp-FMT / #4: Chemical | #5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE CLONED SEQUENCE CONTAINS AN N_TERMINAL VECTOR DERIVED TAG FROM PET 28A, HOWEVER THIS IN NOT ...THE CLONED SEQUENCE CONTAINS AN N_TERMINAL VECTOR DERIVED TAG FROM PET 28A, HOWEVER THIS IN NOT ORDERED IN THE STRUCTURE. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE |
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Crystal grow | Details: 4 M NA FORMATE,20 % GLYCEROL AS CRYOPROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 7, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50.3 Å / Num. obs: 45361 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WCO Resolution: 2.3→49.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.27 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→49.68 Å
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Refine LS restraints |
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