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Yorodumi- PDB-2ahu: Crystal structure of Acyl-CoA transferase (YdiF) apoenzyme from E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ahu | ||||||
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Title | Crystal structure of Acyl-CoA transferase (YdiF) apoenzyme from Escherichia coli O157:H7. | ||||||
Components | putative enzyme ydiF | ||||||
Keywords | TRANSFERASE / YdiF / CoA transferase / Glutamyl thioester / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI | ||||||
Function / homology | Function and homology information acetate CoA-transferase / ketone body catabolic process / short-chain fatty acid metabolic process / acetate CoA-transferase activity / protein homotetramerization Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Rangarajan, E.S. / Li, Y. / Ajamian, E. / Iannuzzi, P. / Kernaghan, S.D. / Fraser, M.E. / Cygler, M. / Matte, A. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystallographic trapping of the glutamyl-CoA thioester intermediate of family I CoA transferases. Authors: Rangarajan, E.S. / Li, Y. / Ajamian, E. / Iannuzzi, P. / Kernaghan, S.D. / Fraser, M.E. / Cygler, M. / Matte, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ahu.cif.gz | 408.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ahu.ent.gz | 347.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ahu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/2ahu ftp://data.pdbj.org/pub/pdb/validation_reports/ah/2ahu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58082.750 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: YdiF / Plasmid: pFO1 / Production host: Escherichia coli (E. coli) / Strain (production host): E.coli DL41 (DE3) References: UniProt: Q8X5X6, Transferases; Transferring sulfur-containing groups; CoA-transferases #2: 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: 2.43 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 7.5 Details: 22.5 % (w/v) PEG 4000, 3% (v/v) isopropanol and 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. all: 491266 / Num. obs: 163843 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.053 / Net I/σ(I): 20.1 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.284 / % possible all: 71.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.12 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.689 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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