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- PDB-2x03: The X-ray structure of the Streptomyces coelicolor A3 Chondroitin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x03 | ||||||
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Title | The X-ray structure of the Streptomyces coelicolor A3 Chondroitin AC Lyase Y253A mutant | ||||||
![]() | PUTATIVE SECRETED LYASE | ||||||
![]() | LYASE / HYALURONATE LYASE / CHONDROITIN LYASE / FAMILY 8 | ||||||
Function / homology | ![]() carbohydrate binding / carbohydrate metabolic process / lyase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Elmabrouk, Z.H. / Taylor, E.J. / Vincent, F. / Smith, N.L. / Turkenburg, J.P. / Davies, G.J. / Black, G.W. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 308.4 KB | Display | ![]() |
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PDB format | ![]() | 249.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2wcoC ![]() 2wdaSC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 82930.141 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-776 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) DSM NO. 40783 Production host: ![]() ![]() #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | THE CLONED SEQUENCE CONTAINS AN N-TERMINAL VECTOR DERIVED TAG FROM PET 28A, HOWEVER THIS IS NOT ...THE CLONED SEQUENCE CONTAINS AN N-TERMINAL VECTOR DERIVED TAG FROM PET 28A, HOWEVER THIS IS NOT ORDERED IN THE STRUCTURE. THERE IS ALSO A SINGLE RESIDUE MUTATION Y253A. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.8 Å3/Da / Density % sol: 74.6 % / Description: NONE |
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Crystal grow | Details: 4.0M NA FORMATE WITH 20% GLYCEROL AS A CRYOPROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 17, 2004 |
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→59.8 Å / Num. obs: 138108 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 13.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WDA Resolution: 2.3→158.55 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.16 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.163 / 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: 24.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→158.55 Å
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Refine LS restraints |
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