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- PDB-4npr: Crystal Structure of the Family 12 Xyloglucanase from Aspergillus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4npr | ||||||
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Title | Crystal Structure of the Family 12 Xyloglucanase from Aspergillus niveus | ||||||
![]() | Xyloglucan-specific endo-beta-1,4-glucanase GH12 | ||||||
![]() | HYDROLASE / b-jelly roll / xyloglucan-specific endo-beta-1 / 4-glucanase | ||||||
Function / homology | ![]() xyloglucan-specific endo-beta-1,4-glucanase / xyloglucan-specific endo-beta-1,4-glucanase activity / cellulase activity / polysaccharide catabolic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cordeiro, R.L. / Santos, C.R. / Furtado, G.P. / Damasio, A.R.L. / Polizeli, M.L.T.M. / Ward, R.J. / Murakami, M.T. | ||||||
![]() | ![]() Title: Crystal Structure of the Family 12 Xyloglucanase from Aspergillus niveus Authors: Santos, C.R. / Cordeiro, R.L. / Furtado, G.P. / Damasio, A.R.L. / Polizeli, M.L.T.M. / Ward, R.J. / 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 | ![]() | 94.4 KB | Display | ![]() |
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PDB format | ![]() | 72.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.8 KB | Display | ![]() |
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Full document | ![]() | 454.2 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vl8S 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26039.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: H6TQN1, xyloglucan-specific endo-beta-1,4-glucanase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.6 Details: 20% PEG 4000, 0.1M ammonium sulfate, 0.1M sodium acetate, pH 3.6, VAPOR DIFFUSION, HANGING 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, 2001 |
Radiation | Monochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 15884 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1450 / % possible all: 91.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VL8 Resolution: 2.5→48.09 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.896 / SU B: 7.821 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.714 / ESU R Free: 0.295 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.941 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.499→2.564 Å / Total num. of bins used: 20
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