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- PDB-2vxm: Screening a Limited Structure-based Library Identifies UDP-GalNAc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vxm | ||||||
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Title | Screening a Limited Structure-based Library Identifies UDP-GalNAc- Specific Mutants of alpha-1,3 Galactosyltransferase | ||||||
![]() | N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE | ||||||
![]() | TRANSFERASE / GLYCOSYLTRANSFERASE / 3 GALACTOSYLTRANSFERASE / TRANSMEMBRANE / GOLGI APPARATUS / ENZYME MECHANISM / GLYCOPROTEIN / METAL-BINDING / SIGNAL-ANCHOR / ALPHA-1 / MEMBRANE / MANGANESE / GLYCOSYLTRANSFERASE GALACTOSYLTRANSFERASE / TRANSFERASE SUBSTRATE SPECIFICITY | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Tumbale, P. / Jamaluddin, H. / Thiyagarajan, N. / Acharya, K.R. / Brew, K. | ||||||
![]() | ![]() Title: Screening a Limited Structure-Based Library Identifies Udp-Galnac-Specific Mutants of {Alpha}-1,3-Galactosyltransferase. Authors: Tumbale, P. / Jamaluddin, H. / Thiyagarajan, N. / Acharya, K.R. / Brew, K. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 219.1 KB | Display | ![]() |
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PDB format | ![]() | 176 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.4 KB | Display | ![]() |
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Full document | ![]() | 532.5 KB | Display | |
Data in XML | ![]() | 45 KB | Display | |
Data in CIF | ![]() | 60.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vxlC ![]() 2jcjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32172.146 Da / Num. of mol.: 4 / Fragment: RESIDUES 82-354 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14769, N-acetyllactosaminide 3-alpha-galactosyltransferase #2: Chemical | ChemComp-MPD / ( | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, HIS 280 TO ARG ENGINEERED RESIDUE IN CHAIN B, HIS 280 TO ARG ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 8 Details: PROTEIN: 5 MG/ML IN THE PRESENCE OF 10 MM MNCL2 AND 10 MM UDP-GAL MOTHER LIQUOR: 0-50% PEG 4000, 0.1 M TRIS-HCL, PH 8.0 AND 0.2 M SODIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 10, 2006 / Details: MIRROR |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.808 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 33047 / % possible obs: 83.8 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 6.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.38 |
Reflection shell | Resolution: 2.8→2.91 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.04 / % possible all: 25.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2JCJ Resolution: 2.82→32.93 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.3448 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.82→32.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→2.99 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: GOL-MPD.TOP |