+Open data
-Basic information
Entry | Database: PDB / ID: 1czf | ||||||
---|---|---|---|---|---|---|---|
Title | ENDO-POLYGALACTURONASE II FROM ASPERGILLUS NIGER | ||||||
Components | POLYGALACTURONASE II | ||||||
Keywords | HYDROLASE / BETA HELIX | ||||||
Function / homology | Function and homology information endo-polygalacturonase / polygalacturonase activity / cell wall organization / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Aspergillus niger (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.68 Å | ||||||
Authors | van Santen, Y. / Kalk, K.H. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: 1.68-A crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis. Authors: van Santen, Y. / Benen, J.A. / Schroter, K.H. / Kalk, K.H. / Armand, S. / Visser, J. / Dijkstra, B.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1czf.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1czf.ent.gz | 121.1 KB | Display | PDB format |
PDBx/mmJSON format | 1czf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/1czf ftp://data.pdbj.org/pub/pdb/validation_reports/cz/1czf | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
3 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37715.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / Secretion: EXTRACELLULAR / Variant: NW156 / References: UniProt: P26214, endo-polygalacturonase #2: Sugar | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.6 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 4000, zinc sulphate, sodium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 46.8 % | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 17, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→30 Å / Num. all: 69332 / Num. obs: 69332 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.22 |
Reflection shell | Resolution: 1.68→1.7 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.07 / Num. unique all: 2421 / % possible all: 64.9 |
Reflection | *PLUS Num. measured all: 263929 |
Reflection shell | *PLUS % possible obs: 64.9 % / Rmerge(I) obs: 0.078 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.68→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |