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Yorodumi- PDB-1k4v: 1.53 A Crystal Structure of the Beta-Galactoside-alpha-1,3-galact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k4v | ||||||
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Title | 1.53 A Crystal Structure of the Beta-Galactoside-alpha-1,3-galactosyltransferase in Complex with UDP | ||||||
Components | N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / Alpha-1 / 3-Galactosyltransferase-UDP COMPLEX | ||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Boix, E. / Swaminathan, G.J. / Zhang, Y. / Natesh, R. / Brew, K. / Acharya, K.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Structure of UDP complex of UDP-galactose:beta-galactoside-alpha -1,3-galactosyltransferase at 1.53-A resolution reveals a conformational change in the catalytically important C terminus. Authors: Boix, E. / Swaminathan, G.J. / Zhang, Y. / Natesh, R. / Brew, K. / Acharya, K.R. | ||||||
History |
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Remark 600 | HETEROGEN UDP 401 and GOL 404 correspond to chain A and, UDP 1401 and GOL 1404 correspond to chain B. | ||||||
Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS A MONOMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k4v.cif.gz | 287.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k4v.ent.gz | 227.5 KB | Display | PDB format |
PDBx/mmJSON format | 1k4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/1k4v ftp://data.pdbj.org/pub/pdb/validation_reports/k4/1k4v | HTTPS FTP |
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-Related structure data
Related structure data | 1g93S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34090.164 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN (80-368) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pSV-SPORT / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P14769, EC: 2.4.1.151 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.9 % Description: THE SECOND MOLECULE IN THE ASYMMETRIC UNIT, NAMED AS B CHAIN HAS NUMBERS STARTING WITH 1000, IN ACCORDANCE WITH SHELXL CONVENTIONS. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG6000, TRIS/HCL, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.909 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.909 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→40 Å / Num. all: 114924 / Num. obs: 114924 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.37 % / Biso Wilson estimate: 14.319 Å2 / Rsym value: 0.106 / Net I/σ(I): 11.73 |
Reflection shell | Resolution: 1.53→1.58 Å / Mean I/σ(I) obs: 1.98 / Num. unique all: 10936 / Rsym value: 0.497 / % possible all: 93.8 |
Reflection | *PLUS Num. measured all: 386939 / Rmerge(I) obs: 0.106 |
Reflection shell | *PLUS % possible obs: 93.8 % / Rmerge(I) obs: 0.497 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G93 Resolution: 1.53→40 Å / Num. parameters: 50327 / Num. restraintsaints: 61066 / Isotropic thermal model: ANISOTROPIC / Cross valid method: Free R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.05 Å2 | |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 19 / Occupancy sum hydrogen: 4647 / Occupancy sum non hydrogen: 5567 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→40 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.1405 / Rfactor Rfree: 0.1906 / Rfactor Rwork: 0.1405 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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