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- PDB-6p2m: Crystal structure of the Caldicellulosiruptor lactoaceticus GH74 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6p2m | |||||||||
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Title | Crystal structure of the Caldicellulosiruptor lactoaceticus GH74 (ClGH74a) enzyme in complex with LLG xyloglucan | |||||||||
![]() | Type 3a cellulose-binding domain protein | |||||||||
![]() | HYDROLASE / glycosyl hydrolase / GH74 / xyloglucanase / 7-fold beta-propeller | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Stogios, P.J. / Skarina, T. / Arnal, G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74. Authors: Arnal, G. / Stogios, P.J. / Asohan, J. / Attia, M.A. / Skarina, T. / Viborg, A.H. / Henrissat, B. / Savchenko, A. / Brumer, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 306.4 KB | Display | ![]() |
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PDB format | ![]() | 239.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6p2kC ![]() 6p2lC ![]() 6p2nC ![]() 6p2oC ![]() 5fkqS C: citing same article ( 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 74671.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Calla_2311 / Plasmid: pMCSG53 / Production host: ![]() ![]() |
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#2: Polysaccharide | beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D- ...beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 1186 molecules ![](data/chem/img/PE3.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PE3 / | ||||
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#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% (w/v) PEG3350, 0.1 M Tris pH 8.5, xyloglucan mixture |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→25 Å / Num. obs: 50820 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.063 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.873 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2479 / CC1/2: 0.623 / Rpim(I) all: 0.438 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5fkq Resolution: 1.98→24.608 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→24.608 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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