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Yorodumi- PDB-2cj4: Crystal Structure of a Cell Wall Invertase Inhibitor from Tobacco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cj4 | ||||||
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Title | Crystal Structure of a Cell Wall Invertase Inhibitor from Tobacco at pH 4.6 | ||||||
Components | INVERTASE INHIBITOR | ||||||
Keywords | INHIBITOR / PROTEIN BINDING / FOUR-HELIX BUNDLE / HELICAL HAIRPIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | NICOTIANA TABACUM (common tobacco) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Hothorn, M. / Scheffzek, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Multiple Crystal Forms of the Cell Wall Invertase Inhibitor from Tobacco Support High Conformational Rigidity Over a Broad Ph-Range Authors: Hothorn, M. / Scheffzek, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cj4.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cj4.ent.gz | 105.3 KB | Display | PDB format |
PDBx/mmJSON format | 2cj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/2cj4 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/2cj4 | HTTPS FTP |
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-Related structure data
Related structure data | 2cj5C 2cj6C 2cj7C 2cj8C 1rj1S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16031.401 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NICOTIANA TABACUM (common tobacco) / Tissue: CELL WALL / Plasmid: PETM20 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI DE3 / References: UniProt: O49908 #2: Chemical | ChemComp-ACT / #3: Chemical | #4: 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: 2.8 Å3/Da / Density % sol: 55.4 % |
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Crystal grow | pH: 4.6 / Details: 17% PEG 4000, 0.1 M NAOAC PH 4.6, 0.2 M LI2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9774 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 6, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→19.65 Å / Num. obs: 43726 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.63→1.72 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.1 / % possible all: 81.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RJ1 Resolution: 1.63→19.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.878 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.078 / 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: 9.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.63→19.65 Å
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Refine LS restraints |
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