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Yorodumi- PDB-4ztc: PglE Aminotransferase in complex with External Aldimine, Mutant K184A -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ztc | ||||||
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Title | PglE Aminotransferase in complex with External Aldimine, Mutant K184A | ||||||
Components | Aminotransferase homolog | ||||||
Keywords | TRANSFERASE / aminotransferase / N-N'-diacetylbacillosamine / N-glycosylation pyridoxyl 5'-phosphate | ||||||
Function / homology | Function and homology information UDP-N-acetylbacillosamine transaminase / UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose transaminase activity / polysaccharide biosynthetic process / protein glycosylation / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Riegert, A.S. / Thoden, J.B. / Young, N.M. / Watson, D.C. / Holden, H.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2015 Title: Structure of the external aldimine form of PglE, an aminotransferase required for N,N'-diacetylbacillosamine biosynthesis. Authors: Riegert, A.S. / Young, N.M. / Watson, D.C. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ztc.cif.gz | 100.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ztc.ent.gz | 73.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ztc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ztc_validation.pdf.gz | 727.2 KB | Display | wwPDB validaton report |
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Full document | 4ztc_full_validation.pdf.gz | 731.9 KB | Display | |
Data in XML | 4ztc_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 4ztc_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/4ztc ftp://data.pdbj.org/pub/pdb/validation_reports/zt/4ztc | HTTPS FTP |
-Related structure data
Related structure data | 1o61S S: Starting model for refinement |
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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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43799.203 Da / Num. of mol.: 1 / Mutation: K184A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Plasmid: pET28t / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9S5Y7, UniProt: Q0P9D3*PLUS |
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#2: Chemical | ChemComp-4RA / [( |
#3: Water | ChemComp-HOH / |
Compound details | The sequence differences are substrain specific |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.67 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15-18% PEG3350, 1 mM PLP, 10 mM UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose, 100 mM MOPS, 200 mM tetraethylammoniumchloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Apr 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 26017 / Num. obs: 26017 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/av σ(I): 15.1 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 2.8 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 1O61 Resolution: 2→29.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.242 / SU ML: 0.147 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.193 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.058 Å2
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Refinement step | Cycle: 1 / Resolution: 2→29.61 Å
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Refine LS restraints |
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