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- PDB-4amb: Crystal structure of the glycosyltransferase SnogD from Streptomy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4amb | ||||||
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Title | Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater | ||||||
![]() | SNOGD | ||||||
![]() | TRANSFERASE / POLYKETIDE BIOSYNTHESIS / GT1 FAMILY / NOGALAMYCIN | ||||||
Function / homology | ![]() cellular glucuronidation / UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / enzyme binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Claesson, M. / Siitonen, V. / Dobritzsch, D. / Metsa-Ketela, M. / Schneider, G. | ||||||
![]() | ![]() Title: Crystal Structure of the Glycosyltransferase Snogd from the Biosynthetic Pathway of the Nogalamycin in Streptomyces Nogalater. Authors: Claesson, M. / Siitonen, V. / Dobritzsch, D. / Metsa-Ketela, M. / Schneider, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.5 KB | Display | ![]() |
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PDB format | ![]() | 116.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 772 KB | Display | ![]() |
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Full document | ![]() | 780.4 KB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4amgC ![]() 4an4C ![]() 3d0qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.8528, -0.5222, -0.002406), Vector: |
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Components
#1: Protein | Mass: 41946.566 Da / Num. of mol.: 2 / Fragment: RESIDUES 13-390 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-DUD / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % / Description: NONE |
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Crystal grow | pH: 5.2 / Details: 26% (W/V) PEG 3350, 0.1 M CITRATE PH 5.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→60 Å / Num. obs: 23310 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.62→2.76 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / % possible all: 86.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3D0Q Resolution: 2.62→50 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.83 / SU B: 14.565 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.945 Å2
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Refinement step | Cycle: LAST / Resolution: 2.62→50 Å
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Refine LS restraints |
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