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Yorodumi- PDB-2vh9: CRYSTAL STRUCTURE OF NXG1-DELTAYNIIG IN COMPLEX WITH XLLG, A XYLO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vh9 | |||||||||
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Title | CRYSTAL STRUCTURE OF NXG1-DELTAYNIIG IN COMPLEX WITH XLLG, A XYLOGLUCAN DERIVED OLIGOSACCHARIDE | |||||||||
Components | CELLULASE | |||||||||
Keywords | HYDROLASE / GLYCOSIDASE / FAMILY GH16 / TROPAEOLUM MAJUS XYLOGLUCANASE / XLLG OLIGOSACCHARIDE / LOOP MUTANT NXG1-YNIIG / SUBSTRATE COMPLEX / GLYCOSIDE HYDROLASE | |||||||||
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: 2.1 Å | |||||||||
Authors | Czjzek, M. / Mark, P. / Baumann, M.J. / Eklof, J.M. / Michel, G. / Brumer, H. | |||||||||
Citation | Journal: Proteins / Year: 2009 Title: Analysis of Nasturtium Tmnxg1 Complexes by Crystallography and Molecular Dynamics Provides Detailed Insight Into Substrate Recognition by Family Gh16 Xyloglucan Endo-Transglycosylases and Endo-Hydrolases. Authors: Mark, P. / Baumann, M.J. / Eklof, J.M. / Gullfot, F. / Michel, G. / Kallas, A.M. / Teeri, T.T. / Brumer, H. / Czjzek, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vh9.cif.gz | 138.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vh9.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vh9_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 2vh9_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 2vh9_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 2vh9_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/2vh9 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/2vh9 | HTTPS FTP |
-Related structure data
Related structure data | 2uwbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.49973, -0.86618, 0.00027), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32982.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TROPAEOLUM MAJUS (nasturtium) / Tissue: SEEDLING / Production host: PICHIA PASTORIS (fungus) References: UniProt: Q07524, xyloglucan-specific endo-beta-1,4-glucanase, cellulase |
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-Sugars , 3 types, 8 molecules
#2: Polysaccharide | beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | |
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-Non-polymers , 3 types, 519 molecules
#4: Chemical | #5: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE LOOP YNIIG (RESIDUES 122-126) HAS BEEN DELETED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 Details: THE PROTEIN CRYSTALLIZED IN SITTING DROPS (CORNING 96 WELL PLATE) MIXING 300 NL OF PROTEIN SOLUTION WITH 150 NL OF WELL SOLUTION CONTAINING 0.2 M MAGNESIUM CHLORIDE, 0.1 M MES BUFFER AT PH 6.0 AND 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: 213252 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.7 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UWB Resolution: 2.1→35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.913 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.158 / 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 / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→35 Å
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Refine LS restraints |
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