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Open data
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Basic information
Entry | Database: PDB / ID: 4bq5 | |||||||||
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Title | Structural analysis of an exo-beta-agarase | |||||||||
![]() | B-AGARASE | |||||||||
![]() | HYDROLASE | |||||||||
Function / homology | ![]() beta-agarase / beta-agarase activity / beta-galactosidase complex / beta-galactosidase activity / carbohydrate metabolic process / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pluvinage, B. / Hehemann, J.H. / Boraston, A.B. | |||||||||
![]() | ![]() Title: Substrate Recognition and Hydrolysis by a Family 50 Exo-Beta-Agarase Aga50D from the Marine Bacterium Saccharophagus Degradans Authors: Pluvinage, B. / Hehemann, J.H. / 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 | ![]() | 329.8 KB | Display | ![]() |
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PDB format | ![]() | 263.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 64.8 KB | Display | |
Data in CIF | ![]() | 94.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bq2SC ![]() 4bq3C ![]() 4bq4C S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 84297.227 Da / Num. of mol.: 2 / Fragment: CATALYTIC MODULE, RESIDUES 47-793 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 4 types, 8 molecules ![](data/chem/img/AAL.gif)
![](data/chem/img/GAL.gif)
![](data/chem/img/GAL.gif)
#2: Polysaccharide | 3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | 3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L- ...3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-AAL / | #5: Sugar | ChemComp-GAL / | |
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-Non-polymers , 3 types, 972 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-CA / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | Details: 21% (W/V) PEG 3350, 0.22 M LITHIUM SULFATE, 0.1 M TRIS-HCL, PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MX-300 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.19 Å / Num. obs: 81677 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.7 / % possible all: 96.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BQ2 Resolution: 2.3→39.19 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.854 / SU B: 7.409 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.417 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.308 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→39.19 Å
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Refine LS restraints |
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