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Yorodumi- PDB-1o7q: Roles of Individual Residues of Alpha-1,3 Galactosyltransferases ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o7q | |||||||||
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Title | Roles of Individual Residues of Alpha-1,3 Galactosyltransferases in Substrate Binding and Catalysis | |||||||||
Components | N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE | |||||||||
Keywords | TRANSFERASE / ALPHA-1 / 3-GALACTOSYLTRANSFERASE-UDP COMPLEX / GLYCOSYLTRANSFERASE / GLYCOPROTEIN / TRANSMEMBRANE / NUCLEOTIDE-BINDING PROTEIN / XENOTRANSPLANTATION | |||||||||
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 / MAD / Resolution: 1.3 Å | |||||||||
Authors | Zhang, Y. / Swaminathan, G.J. / Deshpande, A. / Natesh, R. / Xie, Z. / Acharya, K.R. / Brew, K. | |||||||||
Citation | Journal: Biochemistry / Year: 2003 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: Journal: J.Biol.Chem. / Year: 2001 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: Journal: Embo J. / Year: 2001 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o7q.cif.gz | 401 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o7q.ent.gz | 330.3 KB | Display | PDB format |
PDBx/mmJSON format | 1o7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/1o7q ftp://data.pdbj.org/pub/pdb/validation_reports/o7/1o7q | HTTPS FTP |
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-Related structure data
Related structure data | 1o7oC 1vztC 1gwwS S: Starting model for refinement C: citing same article (ref.) |
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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
-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.) BOS TAURUS (cattle) / Plasmid: PSV-SPORT / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): DH5-ALPHA / References: UniProt: P14769, EC: 2.4.1.151 #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 963 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-UDP / #6: Water | ChemComp-HOH / | |
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-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 |
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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: 2.55 Å3/Da / Density % sol: 51.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
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 |
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Refinement | Method to determine structure: MAD 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
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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
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Refine LS restraints |
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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
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