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Yorodumi- PDB-4amg: Crystal structure of the glycosyltransferase SnogD from Streptomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4amg | ||||||
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Title | Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater | ||||||
Components | SNOGD | ||||||
Keywords | TRANSFERASE / POLYKETIDE BIOSYNTHESIS / GT1 FAMILY / NOGALAMYCIN | ||||||
Function / homology | Function and homology information cellular glucuronidation / UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / enzyme binding / identical protein binding Similarity search - Function | ||||||
Biological species | STREPTOMYCES NOGALATER (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Claesson, M. / Siitonen, V. / Dobritzsch, D. / Metsa-Ketela, M. / Schneider, G. | ||||||
Citation | Journal: FEBS J. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4amg.cif.gz | 146.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4amg.ent.gz | 113.7 KB | Display | PDB format |
PDBx/mmJSON format | 4amg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4amg_validation.pdf.gz | 446.2 KB | Display | wwPDB validaton report |
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Full document | 4amg_full_validation.pdf.gz | 457.1 KB | Display | |
Data in XML | 4amg_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 4amg_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/4amg ftp://data.pdbj.org/pub/pdb/validation_reports/am/4amg | HTTPS FTP |
-Related structure data
Related structure data | 4ambSC 4an4C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 11 - 389 / Label seq-ID: 21 - 399
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-Components
#1: Protein | Mass: 41973.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: THE PROTEIN WAS SUBJECTED TO METHYLATION. MOST LYSINE RESIDUES AND THE N-TERMINAL AMINO GROUP SHOULD BE DIMETHYLATED. ONLY FOR K384 DIMETHYLATION WAS VISIBLE IN THE ELECTRON DENSITY MAP AND THUS MODELED. Source: (gene. exp.) STREPTOMYCES NOGALATER (bacteria) / Plasmid: PNIC-BSAI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RN61 #2: 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: 2.51 Å3/Da / Density % sol: 51.1 % / Description: NONE |
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Crystal grow | pH: 5.7 Details: 16 % (W/V) PEG 3350, 0.2 M MGCL2, 0.1 M BISTRIS PH 5.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→48.3 Å / Num. obs: 26051 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.59→2.73 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AMB Resolution: 2.59→60 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.365 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.795 / ESU R Free: 0.304 / 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: 45.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.59→60 Å
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Refine LS restraints |
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