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Open data
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Basic information
Entry | Database: PDB / ID: 4bq3 | ||||||
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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 | ![]() | 635.5 KB | Display | ![]() |
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PDB format | ![]() | 522.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 127.8 KB | Display | |
Data in CIF | ![]() | 187.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bq2SC ![]() 4bq4C ![]() 4bq5C 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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Unit cell |
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Components
#1: Protein | Mass: 84298.211 Da / Num. of mol.: 4 / Fragment: CATALYTIC MODULE, RESIDUES 47-793 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-47N / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CA / #5: 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: 51 % / Description: NONE |
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Crystal grow | Details: 19% (W/V) PEG 3350, 0.22 M LITHIUM SULFATE, 0.1 M TRIS-HCL, PH 8.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→38.98 Å / Num. obs: 194325 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.8 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BQ2 Resolution: 2.1→38.98 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.235 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.168 / 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: 20.749 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→38.98 Å
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Refine LS restraints |
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