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- PDB-1urx: Crystallographic structure of beta-agarase A in complex with olig... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1urx | |||||||||
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Title | Crystallographic structure of beta-agarase A in complex with oligoagarose | |||||||||
![]() | BETA-AGARASE A | |||||||||
![]() | HYDROLASE / BETA-AGARASE / AGAROSE / GLYCOSIDE HYDROLASE / FAMILY 16 / DOUBLE HELIX / TWO BINDING-SITES | |||||||||
Function / homology | ![]() beta-agarase / beta-agarase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Allouch, J. / Helbert, W. / Henrissat, B. / Czjzek, M. | |||||||||
![]() | ![]() Title: Parallel Substrate Binding Sites in a Beta-Agarase Suggest a Novel Mode of Action on Double-Helical Agarose Authors: Allouch, J. / Helbert, W. / Henrissat, B. / Czjzek, M. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.1 KB | Display | ![]() |
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PDB format | ![]() | 58.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 924.2 KB | Display | ![]() |
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Full document | ![]() | 929.7 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 26 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o4yS S: Starting model for refinement |
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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: 32135.389 Da / Num. of mol.: 1 / Fragment: BETA-AGARASE A DOMAIN, RESIDUES 20-290 / Mutation: YES Source method: isolated from a genetically manipulated source Details: TWO MOLECULES OF OLIGOAGAROSE / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9RGX9, UniProt: G0L322*PLUS, beta-agarase |
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#2: 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)-alpha-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-(1-4)-3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose Source method: isolated from a genetically manipulated source |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293.65 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30 % PEG 4000 200 MM AMMONIUM ACETATE, 100 MM SODIUM ACETATE PH 4.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20.5 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Mar 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→37.2 Å / Num. obs: 34045 / % possible obs: 95.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.8 / % possible all: 98.4 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 37.2 Å / Redundancy: 4.4 % / Num. measured all: 148960 / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS % possible obs: 98.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1O4Y Resolution: 1.7→37.2 Å / SU B: 1.641 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.092
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Displacement parameters | Biso mean: 13.555 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→37.2 Å
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Refinement | *PLUS Num. reflection obs: 32767 / % reflection Rfree: 5 % / Rfactor Rfree: 0.182 / Rfactor Rwork: 0.155 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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