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Yorodumi- PDB-4irp: Crystal structure of catalytic domain of human beta1,4-galactosyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4irp | ||||||
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Title | Crystal structure of catalytic domain of human beta1,4-galactosyltransferase-7 in open conformation with manganses and UDP | ||||||
Components | Beta-1,4-galactosyltransferase 7 | ||||||
Keywords | TRANSFERASE / GT-A fold / open conformation / manganese and UDP complex / glycosyltransferase / Golgi | ||||||
Function / homology | Function and homology information xylosylprotein 4-beta-galactosyltransferase / xylosylprotein 4-beta-galactosyltransferase activity / glycosylation / galactosyltransferase activity / Defective B4GALT7 causes EDS, progeroid type / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / A tetrasaccharide linker sequence is required for GAG synthesis / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / glycosaminoglycan metabolic process ...xylosylprotein 4-beta-galactosyltransferase / xylosylprotein 4-beta-galactosyltransferase activity / glycosylation / galactosyltransferase activity / Defective B4GALT7 causes EDS, progeroid type / beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity / A tetrasaccharide linker sequence is required for GAG synthesis / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / glycosaminoglycan metabolic process / proteoglycan metabolic process / protein N-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / supramolecular fiber organization / negative regulation of fibroblast proliferation / protein modification process / manganese ion binding / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Tsutsui, Y. / Ramakrishnan, B. / Qasba, P.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Crystal Structures of beta-1,4-Galactosyltransferase 7 Enzyme Reveal Conformational Changes and Substrate Binding. Authors: Tsutsui, Y. / Ramakrishnan, B. / Qasba, P.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4irp.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4irp.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 4irp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/4irp ftp://data.pdbj.org/pub/pdb/validation_reports/ir/4irp | HTTPS FTP |
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-Related structure data
Related structure data | 4irqC 4lw3C 4lw6C 4m4kC 3lw6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29216.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: human galectin 1 as fusion protein / Source: (gene. exp.) Homo sapiens (human) Gene: 4galactosyltransferase, B4GALT7, beta1, UNQ748/PRO1478, XGALT1 Plasmid: PET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q9UBV7, Transferases; Glycosyltransferases; Hexosyltransferases, xylosylprotein 4-beta-galactosyltransferase |
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-Non-polymers , 5 types, 305 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-IMD / | #6: 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: 2.93 Å3/Da / Density % sol: 57.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.7 to 1.0 M Sodium accetate, 100 mM imidazole.HCL pH 6.5 as precipating agent, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 17, 2012 / Details: Mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 44450 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 13.1 % / Rsym value: 0.063 / Net I/σ(I): 36.5 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.493 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LW6 Resolution: 2.1→44.26 Å / SU ML: 0.24 / σ(F): 0.55 / Phase error: 31.55 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.26 Å
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Refine LS restraints |
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LS refinement shell |
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