[English] 日本語
![](img/lk-miru.gif)
- PDB-1pzy: W314A-BETA1,4-GALACTOSYLTRANSFERASE-I COMPLEXED WITH ALPHA-LACTAL... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1pzy | ||||||
---|---|---|---|---|---|---|---|
Title | W314A-BETA1,4-GALACTOSYLTRANSFERASE-I COMPLEXED WITH ALPHA-LACTALBUMIN IN THE PRESENCE OF N-ACETYLGLUCOSAMINE, UDP AND MANGANESE | ||||||
![]() |
| ||||||
![]() | TRANSFERASE ACTIVATOR/TRANSFERASE / Beta1 / 4-Galactosyltransferase-I Tryptophan Mutant / Flexible loop Conformation / Protease Digetion / Substrate Binding / ![]() | ||||||
Function / homology | ![]() Lactose synthesis / protein galactosylation / Keratan sulfate biosynthesis / Interaction With Cumulus Cells And The Zona Pellucida / Lactose synthesis / N-Glycan antennae elongation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ramasamy, V. / Ramakrishnan, B. / Boeggeman, E. / Qasba, P.K. | ||||||
![]() | ![]() Title: The Role of Tryptophan 314 in the Conformational Changes of beta 1,4-Galactosyltransferase-I Authors: Ramasamy, V. / Ramakrishnan, B. / Boeggeman, E. / Qasba, P.K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 178.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 139.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1pztC ![]() 1nmmS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
2 | ![]()
| ||||||||||
Unit cell |
| ||||||||||
Details | CHAINS A AND B FORM FIRST, C AND D FORMS SECOND LACTOSE SYNTHASE COMPLEX |
-
Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | ![]() Mass: 14015.835 Da / Num. of mol.: 2 / Fragment: REGULATORY SUBUNIT OF LACTOSE SYNTHASE Source method: isolated from a genetically manipulated source Details: CHAINS A AND B FORM FIRST, B AND D SECOND LACTOSE SYNTHASE COMPLEX Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein | Mass: 32734.449 Da / Num. of mol.: 2 / Fragment: Catalytic Domain, residues 130-402 / Mutation: W314A, C342T Source method: isolated from a genetically manipulated source Details: CHAINS C AND D FORM FIRST, B AND D SECOND LACTOSE SYNTHASE COMPLEX Source: (gene. exp.) ![]() ![]() ![]() Description: N-TERMINAL CARRIES A TAG CONTAINING 13 AMINO ACIDS Plasmid: pET23a / Species (production host): Escherichia coli / Production host: ![]() ![]() ![]() References: UniProt: P08037, ![]() ![]() |
---|
-Sugars , 1 types, 2 molecules ![](data/chem/img/NAG.gif)
#4: Sugar | ![]() |
---|
-Non-polymers , 4 types, 257 molecules ![](data/chem/img/CA.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 | #5: Chemical | #6: Chemical | ![]() #7: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.3 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 11% PEG 4000, 0.1M Sodium chloride and 0.1M Sodium citrate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 31, 2002 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→25 Å / Num. obs: 46294 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 28.9 Å2 / Rsym value: 0.07 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4427 / Rsym value: 0.48 / % possible all: 93.4 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 25 Å / Num. obs: 47881 / Num. measured all: 161993 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 93.4 % / Rmerge(I) obs: 0.48 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 1NMM Resolution: 2.3→19.95 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.1219 Å2 / ksol: 0.327069 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.1 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.37 Å / Luzzati sigma a free: 0.44 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.95 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 25 Å / Rfactor Rfree![]() | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|