[English] 日本語
![](img/lk-miru.gif)
- PDB-4d6d: Crystal structure of a family 98 glycoside hydrolase catalytic mo... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4d6d | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the blood group A-trisaccharide (X02 mutant) | |||||||||
![]() | GLYCOSIDE HYDROLASE | |||||||||
![]() | HYDROLASE / GLYCOSIDE HYDROLASE / BLOOD GROUP ANTIGEN | |||||||||
Function / homology | ![]() family 98 glycoside hydrolase / arginine biosynthesis bifunctional protein fold / Polysaccharide lyase family 8-like, C-terminal / Chondroitinase Ac; Chain A, domain 3 / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kwan, D.H. / Constantinescu, I. / Chapanian, R. / Higgins, M.A. / Samain, E. / Boraston, A.B. / Kizhakkedathu, J.N. / Withers, S.G. | |||||||||
![]() | ![]() Title: Towards Efficient Enzymes for the Generation of Universal Blood Through Structure-Guided Directed Evolution. Authors: Kwan, D.H. / Constantinescu, I. / Chapanian, R. / Higgins, M.A. / Koetzler, M. / Samain, E. / Boraston, A.B. / Kizhakkedathu, J.N. / Withers, S.G. | |||||||||
History |
| |||||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 301.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 240.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 917.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 923.8 KB | Display | |
Data in XML | ![]() | 33.7 KB | Display | |
Data in CIF | ![]() | 54.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d6cC ![]() 4d6eC ![]() 4d6fC ![]() 4d6gC ![]() 4d6hC ![]() 4d6iC ![]() 4d6jC ![]() 4d71C ![]() 4d72C ![]() 2wmiS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 69093.602 Da / Num. of mol.: 1 / Fragment: UNP RESDIUES 423-1005 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A5LBQ0, blood-group-substance endo-1,4-beta-galactosidase | ||||||
---|---|---|---|---|---|---|---|
#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose Source method: isolated from a genetically manipulated source | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | BETA-D-GALACTOSE (GAL): PART OF THE BLOOD GROUP A-TRISACCHARIDE PRODUCT. ALPHA-L-FUCOSE (FUC): PART ...BETA-D-GALACTOSE (GAL): PART OF THE BLOOD GROUP A-TRISACCHAR | Sequence details | CATALYTIC MODULE (RESIDUES 421-1006) | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.89 % / Description: NONE |
---|---|
Crystal grow | Details: 15% PEG 3350, 0.2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE TRIHYDRATE PH 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98005 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→48.13 Å / Num. obs: 105928 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.52→1.6 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WMI Resolution: 1.52→48.35 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.059 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.059 / 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: 9.464 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.52→48.35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|