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Yorodumi- PDB-2xqr: Crystal structure of plant cell wall invertase in complex with a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xqr | |||||||||
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Title | Crystal structure of plant cell wall invertase in complex with a specific protein inhibitor | |||||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / APOPLAST / CELL WALL / HYDROLASE / PROTEIN INHIBITOR / SUGAR METABOLISM / GLYCOSIDASE | |||||||||
Function / homology | Function and homology information beta-fructofuranosidase activity / beta-fructofuranosidase / apoplast / enzyme inhibitor activity / defense response to fungus / cell wall organization / response to wounding / carbohydrate metabolic process / plasma membrane Similarity search - Function | |||||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) NICOTIANA TABACUM (common tobacco) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å | |||||||||
Authors | Hothorn, M. / Van den Ende, W. / Lammens, W. / Rybin, V. / Scheffzek, K. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural Insights Into the Ph-Controlled Targeting of Plant Cell-Wall Invertase by a Specific Inhibitor Protein. Authors: Hothorn, M. / Van Den Ende, W. / Lammens, W. / Rybin, V. / Scheffzek, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xqr.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2xqr.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 2xqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xqr_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 2xqr_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 2xqr_validation.xml.gz | 146.1 KB | Display | |
Data in CIF | 2xqr_validation.cif.gz | 199 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/2xqr ftp://data.pdbj.org/pub/pdb/validation_reports/xq/2xqr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
-Protein , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein | Mass: 61103.039 Da / Num. of mol.: 6 / Fragment: RESIDUES 48-584 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PPICZ / Production host: PICHIA PASTORIS (fungus) / References: UniProt: Q43866, beta-fructofuranosidase #2: Protein | Mass: 15900.205 Da / Num. of mol.: 6 / Fragment: RESIDUES 19-166 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NICOTIANA TABACUM (common tobacco) / Plasmid: PETM20 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ORIGAMI / References: UniProt: O49908 |
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-Sugars , 4 types, 24 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-FRU / #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 804 molecules
#6: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-EPE / #9: Water | ChemComp-HOH / | |
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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: 2.79 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 15% PEG 5000 MME 0.2 M NH4SO4 0.1 M MES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97916 | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 9, 2006 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.58→48.57 Å / Num. obs: 156347 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.9 | |||||||||||||||
Reflection shell | Resolution: 2.58→2.73 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.95 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1RJ1 AND 2AC1 Resolution: 2.58→48.57 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.898 / SU B: 20.113 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.056 / 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: 31.262 Å2
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Refinement step | Cycle: LAST / Resolution: 2.58→48.57 Å
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Refine LS restraints |
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