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Yorodumi- PDB-1vzx: Roles of active site tryptophans in substrate binding and catalys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vzx | |||||||||
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Title | Roles of active site tryptophans in substrate binding and catalysis by ALPHA-1,3 GALACTOSYLTRANSFERASE | |||||||||
Components | N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE | |||||||||
Keywords | TRANSFERASE / ALPHA-1 / 3-GALACTOSYLTRANSFERASE-UDP COMPLEX / GLYCOSYLTRANSFERASE / GLYCOPROTEIN / TRANSMEMBRANE | |||||||||
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: 1.97 Å | |||||||||
Authors | Zhang, Y. / Deshpande, A. / Xie, Z. / Natesh, R. / Acharya, K.R. / Brew, K. | |||||||||
Citation | Journal: Glycobiology / Year: 2004 Title: Roles of active site tryptophans in substrate binding and catalysis by alpha-1,3 galactosyltransferase. Authors: Zhang, Y. / Deshpande, A. / Xie, Z. / Natesh, R. / Acharya, K.R. / Brew, K. #1: 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. #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. #3: 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vzx.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vzx.ent.gz | 114.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vzx_validation.pdf.gz | 630.9 KB | Display | wwPDB validaton report |
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Full document | 1vzx_full_validation.pdf.gz | 635.8 KB | Display | |
Data in XML | 1vzx_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 1vzx_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/1vzx ftp://data.pdbj.org/pub/pdb/validation_reports/vz/1vzx | HTTPS FTP |
-Related structure data
Related structure data | 1vzuC 1k4vS 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: 34067.129 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 80-368 / Mutation: YES Source method: isolated from a genetically manipulated source Details: RESIDUE W314Y / Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PSV-SPORT / Production host: Escherichia coli DH5[alpha] (bacteria) / 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, 648 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #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: 2.92 Å3/Da / Density % sol: 57.94 % |
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Crystal grow | pH: 8 / Details: PEG6000, TRIS/HCL, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→50 Å / Num. obs: 44358 / % possible obs: 98.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.04 |
Reflection shell | Resolution: 2.11→2.19 Å / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K4V Resolution: 1.97→50 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.97→50 Å
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Refine LS restraints |
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Xplor file |
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