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- PDB-2ebs: Crystal Structure Anaalysis of Oligoxyloglucan reducing-end-speci... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ebs | |||||||||
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Title | Crystal Structure Anaalysis of Oligoxyloglucan reducing-end-specific cellobiohydrolase (OXG-RCBH) D465N Mutant Complexed with a Xyloglucan Heptasaccharide | |||||||||
![]() | Oligoxyloglucan reducing end-specific cellobiohydrolase | |||||||||
![]() | HYDROLASE / BETA-PROPELLER / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | ![]() oligoxyloglucan reducing-end-specific cellobiohydrolase / oligoxyloglucan reducing-end-specific cellobiohydrolase activity / xyloglucan metabolic process / cellulose catabolic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yaoi, K. / Kondo, H. / Hiyoshi, A. / Noro, N. / Sugimoto, H. / Miyazaki, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
![]() | ![]() Title: The Structural Basis for the Exo-mode of Action in GH74 Oligoxyloglucan Reducing End-specific Cellobiohydrolase. Authors: Yaoi, K. / Kondo, H. / Hiyoshi, A. / Noro, N. / Sugimoto, H. / Tsuda, S. / Mitsuishi, Y. / Miyazaki, K. #1: ![]() Title: Tandem repeat of a seven-bladed beta-propeller domain in oligoxyloglucan reducing-end-specific cellobiohydrolase Authors: Yaoi, K. / Kondo, H. / Noro, N. / Suzuki, M. / Tsuda, S. / Mitsuishi, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 324.1 KB | Display | ![]() |
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PDB format | ![]() | 258.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 63.2 KB | Display | |
Data in CIF | ![]() | 94.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sqjS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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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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Components
#1: Protein | Mass: 84973.742 Da / Num. of mol.: 2 / Fragment: residues 1-789 / Mutation: D465N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8J0D2, oligoxyloglucan reducing-end-specific cellobiohydrolase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 100mM MES pH5.2-5.3, 5-6% (w/v) PEG 3000, 40% (w/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2004 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 72255 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 6.1 / % possible all: 82.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SQJ Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.525 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.347 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.134 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.461 Å / Total num. of bins used: 20
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