[English] 日本語
![](img/lk-miru.gif)
- PDB-1o7q: Roles of Individual Residues of Alpha-1,3 Galactosyltransferases ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1o7q | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Roles of Individual Residues of Alpha-1,3 Galactosyltransferases in Substrate Binding and Catalysis | |||||||||
![]() | N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE | |||||||||
![]() | TRANSFERASE / ALPHA-1 / 3-GALACTOSYLTRANSFERASE-UDP COMPLEX / GLYCOSYLTRANSFERASE / GLYCOPROTEIN / TRANSMEMBRANE / NUCLEOTIDE-BINDING PROTEIN / XENOTRANSPLANTATION | |||||||||
Function / homology | ![]() N-acetyllactosaminide 3-alpha-galactosyltransferase / N-acetyllactosaminide 3-alpha-galactosyltransferase activity / Golgi cisterna / lipid glycosylation / Golgi cisterna membrane / glycosyltransferase activity / protein glycosylation / vesicle / carbohydrate metabolic process / Golgi apparatus / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, Y. / Swaminathan, G.J. / Deshpande, A. / Natesh, R. / Xie, Z. / Acharya, K.R. / Brew, K. | |||||||||
![]() | ![]() Title: Roles of Individual Enzyme-Substrate Interactions by Alpha-1,3-Galactosyltransferase in Catalysis and Specificity. Authors: Zhang, Y. / Swaminathan, G.J. / Deshpande, A. / Boix, E. / Natesh, R. / Xie, Z. / Acharya, K.R. / Brew, K. #1: ![]() Title: Udp-Galactose:Beta-Galactoside-Alpha-1,3-Galactosyl Transferase at1.53-A Resolution Reveals a Conformational Change in Thecatalytically Important C Terminus Authors: Boix, E. / Swaminathan, G.J. / Zhang, Y. / Natesh, R. / Brew, K. / Acharya, K.R. #2: ![]() Title: Bovine Alpha1,3-Galactosyltransferase Catalytic Domain Structure and its Relationship with Abo Hhisto-Blood Group and Glycophingolipid Glycosyltransferases Authors: Gastinal, L.N. / Bignon, C. / Misra, A.K. / Hindsgaul, O. / Shaper, J.H. / Joziasse, D.H. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 401 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 330.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 731.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 743.1 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o7oC ![]() 1vztC ![]() 1gwwS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 34090.164 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 80-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 4 types, 963 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-UDP / #6: Water | ChemComp-HOH / | |
---|
-Details
Compound details | TRANSFER OF GALACTOSE FROM UDP-GALACTOSE TO AN ACCEPTOR MOLECULE UDP-GALACTOSE + BETA-D-GALACTOSYL- ...TRANSFER OF GALACTOSE FROM UDP-GALACTOSE TO AN ACCEPTOR MOLECULE UDP-GALACTOSE + BETA-D-GALACTOSYL |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.5 / Details: PEG6000, TRIS/HCL, pH 8.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→40 Å / Num. obs: 184017 / % possible obs: 94.9 % / Redundancy: 5.77 % / Net I/σ(I): 15.85 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 4.23 / % possible all: 67.7 |
Reflection | *PLUS Highest resolution: 1.3 Å / Lowest resolution: 40 Å / Num. measured all: 1062198 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 67.7 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 4.2 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GWW Resolution: 1.3→40 Å / Num. parameters: 53725 / Num. restraintsaints: 65073 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56
| |||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 21 / Occupancy sum hydrogen: 4662 / Occupancy sum non hydrogen: 5881 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→40 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.3 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.154 / Rfactor Rwork: 0.107 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|