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Yorodumi- PDB-4an4: Crystal structure of the glycosyltransferase SnogD from Streptomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4an4 | ||||||
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Title | Crystal structure of the glycosyltransferase SnogD from Streptomyces nogalater | ||||||
Components | GLYCOSYL TRANSFERASEGlycosyltransferase | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / POLYKETIDE BIOSYNTHESIS / GT1 FAMILY / NOGALAMYCIN | ||||||
Function / homology | Function and homology information UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / identical protein binding Similarity search - Function | ||||||
Biological species | STREPTOMYCES NOGALATER (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 4an4.cif.gz | 268.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4an4.ent.gz | 214.8 KB | Display | PDB format |
PDBx/mmJSON format | 4an4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/4an4 ftp://data.pdbj.org/pub/pdb/validation_reports/an/4an4 | HTTPS FTP |
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-Related structure data
Related structure data | 4ambSC 4amgC 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: 0 / Refine code: 0
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 41973.613 Da / Num. of mol.: 4 / Fragment: RESIDUES 13-390 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 BL21(DE3) (bacteria) / References: UniProt: Q9RN61 #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | DEOXYURIDINE-5'-DIPHOSPHATE (DUD): POSITION OF DIPHOSPHATE MOIETY NOT WELL FIXED - DOUBLE ...DEOXYURIDI | Sequence details | N-TERMINAL HIS-TAG | |
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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: 2.37 Å3/Da / Density % sol: 48.18 % / Description: NONE |
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Crystal grow | pH: 6.8 Details: 15 % (W/V) PEG 8000 0.16 M CALCIUM ACETATE 0.08 M SODIUM CACODYLATE PH 6.8 |
-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: 2.7→58.6 Å / Num. obs: 42845 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AMB Resolution: 2.7→60 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.681 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. SEVERAL LOOPS DISORDERED
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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: 68.817 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→60 Å
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Refine LS restraints |
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