[English] 日本語
Yorodumi- PDB-2uwb: Crystal structure of the Nasturtium seedling mutant xyloglucanase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uwb | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Nasturtium seedling mutant xyloglucanase isoform NXG1-delta-YNIIG | ||||||
Components | CELLULASE | ||||||
Keywords | HYDROLASE / XYLOGLUCAN-ENDO-TRANSFERASE / GLYCOSIDE HYDROLASE / LOOP MUTANT NXG1- YNIIG / GLYCOSIDASE / FAMILY GH16 / TROPAEOLUM MAJUS XYLOGLUCANASE | ||||||
Function / homology | Function and homology information xyloglucan:xyloglucosyl transferase / xyloglucan:xyloglucosyl transferase activity / xyloglucan metabolic process / cell wall biogenesis / apoplast / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / metal ion binding Similarity search - Function | ||||||
Biological species | TROPAEOLUM MAJUS (nasturtium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Baumann, M.J. / Eklof, J. / Michel, G. / Kallasa, A. / Teeri, T.T. / Brumer, H. / Czjzek, M. | ||||||
Citation | Journal: Plant Cell / Year: 2007 Title: Structural Evidence for the Evolution of Xyloglucanase Activity from Xyloglucan Endo-Transglycosylases: Biological Implications for Cell Wall Metabolism. Authors: Baumann, M.J. / Eklof, J. / Michel, G. / Kallasa, A. / Teeri, T.T. / Czjzek, M. / Brumer, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2uwb.cif.gz | 122.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2uwb.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 2uwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/2uwb ftp://data.pdbj.org/pub/pdb/validation_reports/uw/2uwb | HTTPS FTP |
---|
-Related structure data
Related structure data | 2uwaSC 2uwcC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 5 / Auth seq-ID: 1 - 266 / Label seq-ID: 2 - 267
NCS oper: (Code: given Matrix: (0.49997, 0.86604, 0.00025), Vector: |
-Components
#1: Protein | Mass: 30454.574 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-145,151-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TROPAEOLUM MAJUS (nasturtium) / Tissue: SEEDLING / Plasmid: PPIC9-NXG1-DELTAYNIIG / Production host: PICHIA PASTORIS (fungus) References: UniProt: Q07524, xyloglucan-specific endo-beta-1,4-glucanase, cellulase #2: Water | ChemComp-HOH / | Sequence details | THE FIRST RESIDUE (CHAIN K, RESIDUE V) IS DUE TO THE CLONING CONSTRUCTION FOR HETEROLOGOUS ...THE FIRST RESIDUE (CHAIN K, RESIDUE V) IS DUE TO THE CLONING CONSTRUCTI | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.62 Å3/Da / Density % sol: 73.4 % / Description: NONE |
---|---|
Crystal grow | pH: 6.5 Details: 1.4 M SODIUM ACETATE AND 100 MM SODIUM-CACODYLATE BUFFER AT PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 2, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→45 Å / Num. obs: 76393 / % possible obs: 100 % / Observed criterion σ(I): 0.5 / Redundancy: 10.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UWA Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.866 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 22.14 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|