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Yorodumi- PDB-2iv3: Crystal structure of AviGT4, a glycosyltransferase involved in Av... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iv3 | ||||||
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Title | Crystal structure of AviGT4, a glycosyltransferase involved in Avilamycin A biosynthesis | ||||||
Components | GLYCOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE / ANTIBIOTICS / FAMILY GT-4 / AVILAMYCIN A | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOMYCES VIRIDOCHROMOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Martinez-Fleites, C. / Proctor, M. / Roberts, S. / Bolam, D.N. / Gilbert, H.J. / Davies, G.J. | ||||||
Citation | Journal: Chem.Biol. / Year: 2006 Title: Insights Into the Synthesis of Lipopolysaccharide and Antibiotics Through the Structures of Two Retaining Glycosyltransferases from Family Gt4 Authors: Martinez-Fleites, C. / Proctor, M. / Roberts, S. / Bolam, D.N. / Gilbert, H.J. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iv3.cif.gz | 262.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iv3.ent.gz | 211 KB | Display | PDB format |
PDBx/mmJSON format | 2iv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iv3_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2iv3_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2iv3_validation.xml.gz | 56.1 KB | Display | |
Data in CIF | 2iv3_validation.cif.gz | 77.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/2iv3 ftp://data.pdbj.org/pub/pdb/validation_reports/iv/2iv3 | HTTPS FTP |
-Related structure data
Related structure data | 2iuySC 2iv7C 2iw1C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 36140.930 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES VIRIDOCHROMOGENES (bacteria) Description: DSM 40721 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93KV2 #2: Chemical | ChemComp-UDP / #3: Chemical | ChemComp-GOL / #4: 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: 2.2 Å3/Da / Density % sol: 41 % |
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Crystal grow | Details: 18% PEG 3350, 0.2M LI2SO4, 0.1M MES PH6.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 56829 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.6 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IUY Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.873 / SU B: 18.759 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.473 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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