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Yorodumi- PDB-1pt8: Crystal structure of the yfdW gene product of E. coli, in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pt8 | ||||||
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Title | Crystal structure of the yfdW gene product of E. coli, in complex with oxalate and acetyl-CoA | ||||||
Components | Hypothetical protein yfdW | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / CoA transferase / oxalate / acetyl-CoA / E. coli | ||||||
Function / homology | Function and homology information formyl-CoA transferase / formyl-CoA transferase activity / oxalate catabolic process / cellular response to acidic pH Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Gruez, A. / Roig-Zamboni, V. / Valencia, C. / Campanacci, V. / Cambillau, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The crystal structure of the Escherichia coli yfdW gene product reveals a new fold of two interlaced rings identifying a wide family of CoA transferases. Authors: Gruez, A. / Roig-Zamboni, V. / Valencia, C. / Campanacci, V. / Cambillau, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pt8.cif.gz | 186.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pt8.ent.gz | 147.2 KB | Display | PDB format |
PDBx/mmJSON format | 1pt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pt8_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1pt8_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1pt8_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 1pt8_validation.cif.gz | 54.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/1pt8 ftp://data.pdbj.org/pub/pdb/validation_reports/pt/1pt8 | HTTPS FTP |
-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: 48412.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli, Shigella flexneri / Genus: Escherichia, Shigella / Species: , / Strain: k12, k12 / Gene: YFDW OR B2374 OR SF2441 / Plasmid: pDest17 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)pLysS / References: UniProt: P69902 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #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: 4.17 Å3/Da / Density % sol: 70.51 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: PEG600, cacodylate,oxalate, acethylCoA , pH 6.5, VAPOR DIFFUSION, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979257 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 9, 2003 / Details: mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979257 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 79388 / Num. obs: 79388 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.114 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.234 / % possible all: 98.3 |
Reflection | *PLUS Rmerge(I) obs: 0.114 |
Reflection shell | *PLUS % possible obs: 98.3 % / Redundancy: 0.234 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Apo-form Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.585 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.144 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.451 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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