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Yorodumi- PDB-2c1f: The structure of the family 11 xylanase from Neocallimastix patri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c1f | ||||||
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Title | The structure of the family 11 xylanase from Neocallimastix patriciarum | ||||||
Components | BIFUNCTIONAL ENDO-1,4-BETA-XYLANASE A | ||||||
Keywords | HYDROLASE / GLYCOSIDASE | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | NEOCALLIMASTIX PATRICIARUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Murray, J.W. / Lewis, R.J. / Gilbert, H.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c1f.cif.gz | 61.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c1f.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 2c1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/2c1f ftp://data.pdbj.org/pub/pdb/validation_reports/c1/2c1f | HTTPS FTP |
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-Related structure data
Related structure data | 2vg9C 2vgdC 1f5jS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) NEOCALLIMASTIX PATRICIARUM (fungus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P29127, endo-1,4-beta-xylanase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | CONSTRUCT CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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