[English] 日本語
Yorodumi- PDB-2cj8: Crystal Structure of a Cell Wall Invertase Inhibitor from Tobacco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cj8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of a Cell Wall Invertase Inhibitor from Tobacco (pH 9.5) | ||||||
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: 2.38 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2cj8.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2cj8.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cj8_validation.pdf.gz | 438.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2cj8_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 2cj8_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 2cj8_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/2cj8 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/2cj8 | HTTPS FTP |
-Related structure data
Related structure data | 2cj4C 2cj5C 2cj6C 2cj7C 1rj1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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-IOD / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 39.9 % |
---|---|
Crystal grow | pH: 9.5 / Details: 18 % PEG 4000, 0.1 M TRICINE PH 9.5, 0.2 M NAI |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.976 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 26, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→19.21 Å / Num. obs: 11192 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.38→2.58 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.4 / % possible all: 99.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RJ1 Resolution: 2.38→19.21 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.859 / SU B: 14.218 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.536 / ESU R Free: 0.302 / 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: 37.44 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→19.21 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|