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Yorodumi- PDB-1dyp: 1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dyp | ||||||
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Title | 1,3-ALPHA-1,4-BETA-D-GALACTOSE-4-SULFATE-3,6-ANHYDRO-D-GALACTOSE 4 GALACTOHYDROLASE | ||||||
Components | KAPPA-CARRAGEENASE | ||||||
Keywords | HYDROLASE / KAPPA-CARRAGEENAN DOUBLE HELIX DEGRADATION | ||||||
Function / homology | Function and homology information kappa-carrageenase / kappa-carrageenase activity / carbohydrate metabolic process / periplasmic space Similarity search - Function | ||||||
Biological species | PSEUDOALTEROMONAS CARRAGEENOVORA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.54 Å | ||||||
Authors | Michel, G. / Chantalat, L. / Dideberg, O. | ||||||
Citation | Journal: Structure / Year: 2001 Title: The Kappa-Carrageenase of P. Carrageenovora Features a Tunnel-Shaped Active Site: A Novel Insight in the Evolution of Clan-B Glycoside Hydrolases Authors: Michel, G. / Chantalat, L. / Duee, E. / Barbeyron, T. / Henrissat, B. / Kloareg, B. / Dideberg, O. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Expression, Purification, Crystallization and Preliminary X-Ray Analysis of the Kappa-Carrageenase from Pseudoalteromonas Carrageenovora. Authors: Michel, G. / Barbeyron, T. / Flament, D. / Vernet, T. / Kloareg, B. / Dideberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dyp.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dyp.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 1dyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dyp_validation.pdf.gz | 361.6 KB | Display | wwPDB validaton report |
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Full document | 1dyp_full_validation.pdf.gz | 363.5 KB | Display | |
Data in XML | 1dyp_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1dyp_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/1dyp ftp://data.pdbj.org/pub/pdb/validation_reports/dy/1dyp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31559.338 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH CADMIUM CHLORIDE Source: (gene. exp.) PSEUDOALTEROMONAS CARRAGEENOVORA (bacteria) Description: PROCESSED PROTEIN, HIS-TAG, SELEMETHIONYL PROTEIN Gene: CGKA / Plasmid: PET20B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P43478, kappa-carrageenase | ||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CL / #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: 2.019 Å3/Da / Density % sol: 40.38 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 285 K / pH: 7.2 / Method: vapor diffusion, hanging dropDetails: Michel, G., (1999) Acta Crystallogr.,Sect.D, D55, 918. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8860, 0.9755, 0.9787 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 16, 1999 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.54→24.25 Å / Num. obs: 38205 / % possible obs: 97.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 12.5 Å2 / Rsym value: 0.03 / Net I/σ(I): 16.1 | ||||||||||||
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 6.2 / Rsym value: 0.116 / % possible all: 81.3 | ||||||||||||
Reflection | *PLUS Redundancy: 3.15 % / Num. measured all: 120447 / Rmerge(I) obs: 0.03 | ||||||||||||
Reflection shell | *PLUS % possible obs: 81.3 % / Rmerge(I) obs: 0.116 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.54→24.25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1371908.26 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE FOLLOWING RESIDUES HAVE TWO CONFORMATIONS, MET 28, SER 199, LYS 277, SER 285, GLU 287.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.427 Å2 / ksol: 0.33629 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.54→24.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.64 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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