+Open data
-Basic information
Entry | Database: PDB / ID: 1pt5 | ||||||
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Title | Crystal structure of gene yfdW of E. coli | ||||||
Components | Hypothetical protein yfdWHypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / transferase / Coenzyme binding / AcetylCoA | ||||||
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 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 | 1pt5.cif.gz | 187.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pt5.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/1pt5 ftp://data.pdbj.org/pub/pdb/validation_reports/pt/1pt5 | 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: 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: 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: 4.16 Å3/Da / Density % sol: 70.46 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: PEG600, cacodylate, acetylCoA, pH 6.5, VAPOR DIFFUSION, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
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: ID14-4 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 8, 2002 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 105732 / Num. obs: 105732 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rsym value: 0.078 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2→2.11 Å / Rsym value: 0.265 / % possible all: 97.5 |
Reflection | *PLUS Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 97.5 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: apo-enzyme Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.088 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.105 / ESU R Free: 0.099 / 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: 23.857 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.168 / Rfactor Rwork: 0.146 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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