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- PDB-5a3h: 2-DEOXY-2-FLURO-B-D-CELLOBIOSYL/ENZYME INTERMEDIATE COMPLEX OF TH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a3h | |||||||||
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Title | 2-DEOXY-2-FLURO-B-D-CELLOBIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.8 ANGSTROMS RESOLUTION | |||||||||
![]() | ENDOGLUCANASE | |||||||||
![]() | HYDROLASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSIDE HYDROLASE FAMILY 5 / MICHAELIS COMPLEX / SKEW-BOAT / DISTORTION | |||||||||
Function / homology | ![]() cellulase / cellulase activity / cellulose catabolic process / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Davies, G.J. / Varrot, A. / Dauter, M. / Brzozowski, A.M. / Schulein, M. / Mackenzie, L. / Withers, S.G. | |||||||||
![]() | ![]() Title: Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase. Authors: Davies, G.J. / Mackenzie, L. / Varrot, A. / Dauter, M. / Brzozowski, A.M. / Schulein, M. / Withers, S.G. #1: ![]() Title: Structure of the Bacillus Agaradherans Family 5 Endoglucanase at 1.6 A and its Cellobiose Complex at 2.0 A Resolution Authors: Davies, G.J. / Dauter, M. / Brzozowski, A.M. / Bjornvad, M.E. / Andersen, K.V. / Schulein, 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 | ![]() | 77.3 KB | Display | ![]() |
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PDB format | ![]() | 59.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 747.4 KB | Display | ![]() |
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Full document | ![]() | 747.3 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a3hC ![]() 4a3hC ![]() 6a3hC ![]() 7a3hC ![]() 1a3hS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33998.023 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN ONLY Source method: isolated from a genetically manipulated source Details: THIS IS A COMPLEX WITH 2-DEOXY-2-FLUOROCELLOBIOSE COVALENTLY LINKED TO THE ENZYMATIC NUCLEOPHILE, GLU 228 Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-beta-cellobiose |
#3: Water | ChemComp-HOH / |
Compound details | CEL5A IS A MEMBER OF GLYCOSIDE HYDROLASE FAMILY 5, IT IS ONE OF THE GH-A CLAN MEMBERS. THIS ENTRY ...CEL5A IS A MEMBER OF GLYCOSIDE HYDROLASE FAMILY 5, IT IS ONE OF THE GH-A CLAN MEMBERS. THIS ENTRY REPRESENTS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.4 % | |||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | |||||||||||||||
Crystal grow | *PLUS pH: 4.5 / Method: vapor diffusion, hanging drop / Details: Davies, G.J., (1998) Biochemistry, 37, 1926. | |||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: YALE/MSC MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→15 Å / Num. obs: 27156 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 14.24 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.82→1.88 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.26 / % possible all: 99.2 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.26 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A3H Resolution: 1.82→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 13.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.14 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |