[English] 日本語
![](img/lk-miru.gif)
- PDB-7esm: Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase f... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7esm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a L-rhamnose-alpha-1,4-D-glucuronate lyase from Fusarium oxysporum 12S, L-Rha complex | ||||||
![]() | L-rhamnose-alpha-1,4-D-glucuronate lyase | ||||||
![]() | LYASE / seven-bladed beta-propeller | ||||||
Function / homology | ACETATE ION / alpha-L-rhamnopyranose![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kondo, T. / Arakawa, T. / Fushinobu, S. / Sakamoto, T. | ||||||
![]() | ![]() Title: Structural and functional analysis of gum arabic l-rhamnose-alpha-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family. Authors: Kondo, T. / Kichijo, M. / Maruta, A. / Nakaya, M. / Takenaka, S. / Arakawa, T. / Fushinobu, S. / Sakamoto, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 101.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 79.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50085.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: Lyases; Carbon-oxygen lyases; Acting on polysaccharides |
---|
-Sugars , 2 types, 2 molecules ![](data/chem/img/RAM.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Sugar | ChemComp-RAM / |
-Non-polymers , 3 types, 223 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ACT / |
---|---|
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|---|
Sequence details | The amino acid sequence of FoRham1 has been registered in GenBank, DDBj and EMBL. Its accession ...The amino acid sequence of FoRham1 has been registered in GenBank, DDBj and EMBL. Its accession number is LC617219. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.4 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30 % (v/v) PEG 1500, 0.1 M BICINE-NaOH (pH 8.5), 10 % (v/v) 2-propanol, 0.1 M L-Rha, Crystal was soaked into 20 % (v/v) glycerol at 298 K for 1 min |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 8, 2019 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 77482 / % possible obs: 98.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.4→1.42 Å / Num. unique obs: 3830 / CC1/2: 0.882 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.11 Å2 / Biso mean: 15.206 Å2 / Biso min: 6.87 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→41.52 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|