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Yorodumi- PDB-3fsb: Crystal structure of QdtC, the dTDP-3-amino-3,6-dideoxy-D-glucose... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fsb | ||||||
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Title | Crystal structure of QdtC, the dTDP-3-amino-3,6-dideoxy-D-glucose N-acetyl transferase from Thermoanaerobacterium thermosaccharolyticum in complex with CoA and dTDP-3-amino-quinovose | ||||||
Components | QdtC | ||||||
Keywords | TRANSFERASE / N-acetyltransferase / deoxysugar / natural product | ||||||
Function / homology | Function and homology information Ubiquitin Ligase Nedd4; Chain: W; - #30 / Ubiquitin Ligase Nedd4; Chain: W; / : / Hexapeptide repeat of succinyl-transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Other non-globular / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily ...Ubiquitin Ligase Nedd4; Chain: W; - #30 / Ubiquitin Ligase Nedd4; Chain: W; / : / Hexapeptide repeat of succinyl-transferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Other non-globular / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Special / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Thermoanaerobacterium thermosaccharolyticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Holden, H.M. / Thoden, J.B. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural and Functional Studies of QdtC: an N-Acetyltransferase Required for the Biosynthesis of dTDP-3-Acetamido-3,6-Dideoxy-alpha-D-Glucose. Authors: Thoden, J. / Cook, P. / Schaffer, C. / Messner, P. / Holden, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fsb.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fsb.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 3fsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fsb_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3fsb_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3fsb_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 3fsb_validation.cif.gz | 36.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/3fsb ftp://data.pdbj.org/pub/pdb/validation_reports/fs/3fsb | HTTPS FTP |
-Related structure data
Related structure data | 3fs8SC 3fscC 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30816.162 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterium thermosaccharolyticum (bacteria) Strain: E2707-71 / Gene: qdtC / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q6TFC6 #2: Chemical | #3: Chemical | #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: 2.41 Å3/Da / Density % sol: 48.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 24% PEG 5000, 0.1M HEPES, 0.01 M Acetyl-CoA, 0.04M dTDP-3-aminoquinovose, 2% ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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 AXS Platinum135 / Detector: CCD / Date: Aug 1, 2008 / Details: Montel |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 39913 / Num. obs: 39913 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.084 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4815 / Rsym value: 0.264 / % possible all: 79.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3fs8 Resolution: 1.95→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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