[English] 日本語
Yorodumi- PDB-2v8j: Structure of a Family 2 Pectate Lyase in Complex with a Transitio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v8j | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a Family 2 Pectate Lyase in Complex with a Transition Metal | ||||||
Components | PECTATE LYASE | ||||||
Keywords | LYASE / PERIPLASM / PECTATE LYASE / BETA-ELIMINATION / PECTIN DEGRADATION | ||||||
Function / homology | Function and homology information carbon-oxygen lyase activity, acting on polysaccharides / pectin catabolic process / periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | YERSINIA ENTEROCOLITICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Abbott, D.W. / Boraston, A.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: A Family 2 Pectate Lyase Displays a Rare Fold and Transition Metal-Assisted -Elimination. Authors: Abbott, D.W. / Boraston, A.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2v8j.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2v8j.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 2v8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/2v8j ftp://data.pdbj.org/pub/pdb/validation_reports/v8/2v8j | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 60374.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A1JSS8*PLUS, pectate lyase |
---|---|
#2: Chemical | ChemComp-MN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.27 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 113 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5148 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5148 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.91 Å / Num. obs: 153616 / % possible obs: 93.2 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.09 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→20.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.581 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.192 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.88 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→20.01 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|