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- PDB-2c1f: The structure of the family 11 xylanase from Neocallimastix patri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2c1f | ||||||
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Title | The structure of the family 11 xylanase from Neocallimastix patriciarum | ||||||
![]() | BIFUNCTIONAL ENDO-1,4-BETA-XYLANASE A | ||||||
![]() | HYDROLASE / GLYCOSIDASE | ||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Murray, J.W. / Lewis, R.J. / Gilbert, H.J. | ||||||
![]() | ![]() Title: Understanding the Structural Basis for Substrate and Inhibitor Recognition in Eukaryotic Gh11 Xylanases. Authors: Vardakou, M. / Dumon, C. / Murray, J.W. / Christakopoulos, P. / Weiner, D.P. / Juge, N. / Lewis, R.J. / Gilbert, H.J. / Flint, J.E. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.1 KB | Display | ![]() |
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PDB format | ![]() | 43.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.7 KB | Display | ![]() |
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Full document | ![]() | 423.4 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vg9C ![]() 2vgdC ![]() 1f5jS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 26011.660 Da / Num. of mol.: 1 / Fragment: DOMAIN 2, RESIDUES 275-499 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | CONSTRUCT CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % |
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Crystal grow | Details: 0.1M CDCL2, 0.1M SODIUM ACETATE AND 30% V/V PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Apr 14, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→37.04 Å / Num. obs: 15357 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 7.49 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.37 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 2.87 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.07 / % possible all: 82.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1F5J Resolution: 2.1→83.05 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.951 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.159 / 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 / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→83.05 Å
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Refine LS restraints |
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