+Open data
-Basic information
Entry | Database: PDB / ID: 1bhe | ||||||
---|---|---|---|---|---|---|---|
Title | POLYGALACTURONASE FROM ERWINIA CAROTOVORA SSP. CAROTOVORA | ||||||
Components | POLYGALACTURONASE | ||||||
Keywords | GLYCOSIDASE / FAMILY 28 GLYCOSYL HYDROLASE / HYDROLYSES POLYGALACTURONIC ACID | ||||||
Function / homology | Function and homology information endo-polygalacturonase / polygalacturonase activity / cell wall organization / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Pectobacterium carotovorum subsp. carotovorum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å | ||||||
Authors | Pickersgill, R. / Smith, D. / Worboys, K. / Jenkins, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora. Authors: Pickersgill, R. / Smith, D. / Worboys, K. / Jenkins, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1bhe.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1bhe.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/1bhe ftp://data.pdbj.org/pub/pdb/validation_reports/bh/1bhe | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40135.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium carotovorum subsp. carotovorum (bacteria) Species: Pectobacterium carotovorum / Strain: subsp. carotovorum Description: SEE H. HEMILA, R. PAKKANEN, R. HEIKINHEIMO, E. TAPIO PALVA & I. PALVA (1992) GENE 116, 27-33 Production host: Bacillus subtilis (bacteria) / References: UniProt: P26509, endo-polygalacturonase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 42 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 18% PEG 8000, 0.1M SODIUM CACODYLATE, PH 6.5, 0.2M MAGNESIUM ACETATE. | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.9 Å / Num. obs: 31103 / % possible obs: 97 % / Redundancy: 3 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 9 / % possible all: 95 |
Reflection shell | *PLUS % possible obs: 95.2 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 1.9→12.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE DENSITY AND STEREOCHEMISTRY FOR ASP 129 ARE POOR.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→12.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |