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- PDB-4w85: Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4w85 | ||||||
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Title | Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in complex with glucose | ||||||
![]() | Xyloglucan-specific endo-beta-1,4-glucanase | ||||||
![]() | HYDROLASE / glycoside hydrolase / cell wall degrading enzyme / GH5 family | ||||||
Function / homology | ![]() xyloglucan-specific endo-beta-1,4-glucanase / xyloglucan-specific endo-beta-1,4-glucanase activity / glucan catabolic process / beta-glucosidase activity / cell surface / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Santos, C.R. / Cordeiro, R.L. / Wong, D.W.S. / Murakami, M.T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Xyloglucan Specificity and alpha-d-Xylp(1 6)-d-Glcp Recognition at the -1 Subsite within the GH5 Family. Authors: Dos Santos, C.R. / Cordeiro, R.L. / Wong, D.W. / 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 | ![]() | 155.9 KB | Display | ![]() |
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PDB format | ![]() | 120.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4w84C ![]() 4w86C ![]() 4w87C ![]() 4w88C ![]() 4w89C ![]() 4w8aC ![]() 4w8bC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38118.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: cow's rumen Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: D2K7Z0, xyloglucan-specific endo-beta-1,4-glucanase #2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG3350, PEG400, magnesium chloride |
-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, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.459 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.92→50 Å / Num. obs: 75371 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 37.178 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.152 / Rrim(I) all: 0.16 / Χ2: 0.902 / Net I/σ(I): 12.81 / Num. measured all: 806168 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: the native structure of XEG5A Resolution: 1.92→48.85 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.868 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 88.19 Å2 / Biso mean: 29.653 Å2 / Biso min: 17.42 Å2
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Refinement step | Cycle: final / Resolution: 1.92→48.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.918→1.968 Å / Total num. of bins used: 20
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