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- PDB-1gye: Structure of Cellvibrio cellulosa alpha-L-arabinanase complexed w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gye | |||||||||
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Title | Structure of Cellvibrio cellulosa alpha-L-arabinanase complexed with Arabinohexaose | |||||||||
![]() | ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A | |||||||||
![]() | HYDROLASE / ARABINANASE / PROPELLER / CATALYSIS / CELLVIBRIO / PSEUDOMONAS | |||||||||
Function / homology | ![]() arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nurizzo, D. / Turkenburg, J.P. / Charnock, S.J. / Roberts, S.M. / Dodson, E.J. / McKie, V.A. / Taylor, E.J. / Gilbert, H.J. / Davies, G.J. | |||||||||
![]() | ![]() Title: Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold. Authors: Nurizzo, D. / Turkenburg, J.P. / Charnock, S.J. / Roberts, S.M. / Dodson, E.J. / McKie, V.A. / Taylor, E.J. / Gilbert, H.J. / Davies, G.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.8 KB | Display | ![]() |
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PDB format | ![]() | 59.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 726.8 KB | Display | ![]() |
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Full document | ![]() | 731.7 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 20.1 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 35845.191 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P95470*PLUS, arabinan endo-1,5-alpha-L-arabinanase |
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#2: Polysaccharide | alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L- ...alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Sequence details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.2 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 10% PEG8000, 100MM TRIS-HCL PH8.0, 20% GLYCEROL, 100MM ARABINOTRIOSE, pH 8.00 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
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 CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 15610 / % possible obs: 100 % / Redundancy: 10.47 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 10.74 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 6.1 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 100 % / Redundancy: 10.5 % |
Reflection shell | *PLUS % possible obs: 100 % / Redundancy: 10.7 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NATIVE STRUCTURE SOLVED PREVIOUSLY Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.491 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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