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- PDB-4kcb: Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Rumi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kcb | ||||||
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Title | Crystal Structure of Exo-1,5-alpha-L-arabinanase from Bovine Ruminal Metagenomic Library | ||||||
![]() | Arabinan endo-1,5-alpha-L-arabinosidase | ||||||
![]() | HYDROLASE / beta-propeller / GH43 / glycoside hydrolase / arabinanase | ||||||
Function / homology | ![]() arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Santos, C.R. / Polo, C.C. / Costa, M.C.M.F. / Nascimento, A.F.Z. / Wong, D.W.S. / Murakami, M.T. | ||||||
![]() | ![]() Title: Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases. Authors: Santos, C.R. / Polo, C.C. / Costa, M.C. / Nascimento, A.F. / Meza, A.N. / Cota, J. / Hoffmam, Z.B. / Honorato, R.V. / Oliveira, P.S. / Goldman, G.H. / Gilbert, H.J. / Prade, R.A. / Ruller, R. ...Authors: Santos, C.R. / Polo, C.C. / Costa, M.C. / Nascimento, A.F. / Meza, A.N. / Cota, J. / Hoffmam, Z.B. / Honorato, R.V. / Oliveira, P.S. / Goldman, G.H. / Gilbert, H.J. / Prade, R.A. / Ruller, R. / Squina, F.M. / Wong, D.W. / Murakami, M.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.2 KB | Display | ![]() |
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PDB format | ![]() | 106.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.8 KB | Display | ![]() |
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Full document | ![]() | 481.9 KB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 30.9 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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Details | the biological unit is a monomer; there are 2 biological units in asymmetric unit |
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Components
#1: Protein | Mass: 50320.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: THE SAMPLE SEQUENCE WAS IDENTIFIED FROM A DNA LIBRARY CONSTRUCTED FROM BOVINE RUMEN FLUID (WONG ET AL., 2008) Production host: ![]() ![]() References: UniProt: D2XML8, arabinan endo-1,5-alpha-L-arabinanase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Ammonium Phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2013 |
Radiation | Monochromator: Si(111)double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→40 Å / Num. obs: 20619 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.9→3 Å / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.944 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→35.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.896→2.97 Å / Total num. of bins used: 20
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