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Yorodumi- PDB-4k4d: X-ray crystal structure of E. coli YbdB complexed with 2,4-dihydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k4d | ||||||
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Title | X-ray crystal structure of E. coli YbdB complexed with 2,4-dihydroxyphenacyl-CoA | ||||||
Components | Proofreading thioesterase EntH | ||||||
Keywords | HYDROLASE / Hotdog fold / thioeatsrase | ||||||
Function / homology | Function and homology information thiolester hydrolase activity / acyl-CoA hydrolase activity / 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity / enterobactin biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / hydrolase activity, acting on ester bonds / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.17 Å | ||||||
Authors | Ru, W. / Farelli, J.D. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB. Authors: Wu, R. / Latham, J.A. / Chen, D. / Farelli, J. / Zhao, H. / Matthews, K. / Allen, K.N. / Dunaway-Mariano, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k4d.cif.gz | 70.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k4d.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 4k4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k4d_validation.pdf.gz | 923.5 KB | Display | wwPDB validaton report |
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Full document | 4k4d_full_validation.pdf.gz | 932.3 KB | Display | |
Data in XML | 4k4d_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 4k4d_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/4k4d ftp://data.pdbj.org/pub/pdb/validation_reports/k4/4k4d | HTTPS FTP |
-Related structure data
Related structure data | 4k49C 4k4aC 4k4bC 4k4cC 1vh9S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14989.114 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0597, entH, JW0589, ybdB / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P0A8Y8, Hydrolases; Acting on ester bonds; Thioester hydrolases #2: Chemical | #3: Chemical | ChemComp-MLI / | #4: Chemical | #5: 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: 2.16 Å3/Da / Density % sol: 42.97 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.0 M SODIUM MALONATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 28, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→20.4 Å / Num. obs: 14243 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1VH9 Resolution: 2.17→20.4 Å / SU ML: 0.32 / σ(F): 1.89 / Phase error: 30.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.17→20.4 Å
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Refine LS restraints |
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LS refinement shell |
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