+
Open data
-
Basic information
Entry | Database: PDB / ID: 1qcx | ||||||
---|---|---|---|---|---|---|---|
Title | PECTIN LYASE B | ||||||
![]() | PECTIN LYASE B | ||||||
![]() | LYASE / PECTIN LYASE / BETA-HELIX PROTEIN / PECTIN / PLANT CELL WALL | ||||||
Function / homology | ![]() pectin lyase / pectin lyase activity / polysaccharide catabolic process / cell wall organization / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vitali, J. / Jurnak, F. | ||||||
![]() | ![]() Title: The tree-dimensional structure of aspergillus niger pectin lyase B at 1.7-A resolution. Authors: Vitali, J. / Schick, B. / Kester, H.C. / Visser, J. / Jurnak, F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 84.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 63.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 360.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 360.7 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37837.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 41 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5 / Details: pH 5.0 | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 41 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. obs: 50124 / % possible obs: 73.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.054 / Net I/σ(I): 18.9 |
Reflection | *PLUS Num. measured all: 204035 / Rmerge(I) obs: 0.054 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: FOR MOLECULAR REPLACEMENT: PARALLEL BETA HELIX OF PELE, ALL AMINO ACIDS REPLACED WITH ALA UNLESS COMMON IN THE TWO PROTEINS; HEAVY ATOMS: PT, HG Resolution: 1.7→7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: R-FREE / σ(F): 2 Details: FREE R WAS USED UNTIL LAST CYCLE WHEN ALL DATA WAS INCLUDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.78→1.87 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|