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Yorodumi- PDB-5ktd: FdhC with bound products: Coenzyme A and dTDP-3-amino-3,6-dideoxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ktd | ||||||
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Title | FdhC with bound products: Coenzyme A and dTDP-3-amino-3,6-dideoxy-d-glucose | ||||||
Components | FdhC | ||||||
Keywords | TRANSFERASE / GNAT / Sugar / O-antigen | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups / metal ion binding Similarity search - Function | ||||||
Biological species | Acinetobacter nosocomialis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Salinger, A.J. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2016 Title: Structural and Functional Investigation of FdhC from Acinetobacter nosocomialis: A Sugar N-Acyltransferase Belonging to the GNAT Superfamily. Authors: Salinger, A.J. / 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 | 5ktd.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ktd.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ktd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/5ktd ftp://data.pdbj.org/pub/pdb/validation_reports/kt/5ktd | HTTPS FTP |
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-Related structure data
Related structure data | 5ktaSC 5ktcC 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22321.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter nosocomialis (bacteria) / Gene: fdhC / Production host: Escherichia coli (E. coli) / References: UniProt: V5RDR9 |
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-Non-polymers , 5 types, 106 molecules
#2: Chemical | ChemComp-EDO / |
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#3: Chemical | ChemComp-QUH / [[( |
#4: Chemical | ChemComp-COA / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-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: 48.03 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 5 Details: 30% monomethylether poly(ethylene glycol) 5000, 200 mM LiCl, and 100 mM Homo-PIPES |
-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: Dec 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 17505 / % possible obs: 99.7 % / Redundancy: 29.5 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 21.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5kta Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.897 / SU B: 4.733 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.17 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.168 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→50 Å
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Refine LS restraints |
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