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- PDB-1o4z: THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE B FROM ZOBELLIA G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1o4z | ||||||
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Title | THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE B FROM ZOBELLIA GALACTANIVORANS | ||||||
![]() | beta-agarase B | ||||||
![]() | HYDROLASE / BETA-AGARASE / GLYCOSIDE HYDROLASE FAMILY 16 / AGAROSE DEGRADATION / CLEAVAGE OF BETA-1 / 4-D-GALACTOSE LINKAGES | ||||||
Function / homology | ![]() beta-agarase / beta-agarase activity / cell outer membrane / carbohydrate metabolic process / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Allouch, J. / Jam, M. / Helbert, W. / Barbeyron, T. / Kloareg, B. / Henrissat, B. / Czjzek, M. | ||||||
![]() | ![]() Title: The Three-dimensional Structures of Two {beta}-Agarases. Authors: Allouch, J. / Jam, M. / Helbert, W. / Barbeyron, T. / Kloareg, B. / Henrissat, B. / Czjzek, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 272.5 KB | Display | ![]() |
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PDB format | ![]() | 216 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483 KB | Display | ![]() |
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Full document | ![]() | 505.4 KB | Display | |
Data in XML | ![]() | 55.5 KB | Display | |
Data in CIF | ![]() | 79.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 40056.523 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-EPE / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 47 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: 58% methyl-pentane-diol 20 mM calcium chloride 100 mM Hepes , pH 7.5, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20.5 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→95.35 Å / Num. all: 61473 / Num. obs: 61473 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.106 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.339 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 24.8 Å / Num. obs: 64783 / Num. measured all: 428617 / Rmerge(I) obs: 0.106 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.339 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: BETA-AGARASE A Resolution: 2.3→25 Å / SU B: 5.974 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.218
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Displacement parameters | Biso mean: 19.944 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 24.8 Å / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.199 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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