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- PDB-6ptm: Crystal structure of apo exo-carrageenase GH42 from Bacteroides ovatus -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ptm | ||||||
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Title | Crystal structure of apo exo-carrageenase GH42 from Bacteroides ovatus | ||||||
![]() | Uncharacterized protein | ||||||
![]() | HYDROLASE / exo-carrageenase | ||||||
Function / homology | Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / beta-galactosidase complex / beta-galactosidase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / Glyco_hydro_42 domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hettle, A.G. / Boraston, A.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Insights into the kappa / iota-carrageenan metabolism pathway of some marinePseudoalteromonasspecies. Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. ...Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. / Van Hamme, J. / Boraston, A.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.3 KB | Display | ![]() |
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PDB format | ![]() | 129.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6pnuC ![]() 6popC ![]() 6prmC ![]() 6psmC ![]() 6psoC ![]() 6pt4C ![]() 6pt6C ![]() 6pt9C ![]() 6ptkC C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 88592.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HMPREF1069_02044 / Plasmid: pET28a / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 400, Tris, MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2→54.66 Å / Num. obs: 57229 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4129 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.36 Å2 / Biso mean: 20.083 Å2 / Biso min: 10.29 Å2
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Refinement step | Cycle: final / Resolution: 2→50.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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