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Yorodumi- PDB-1ym5: Crystal structure of YHI9, the yeast member of the phenazine bios... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ym5 | ||||||
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Title | Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily. | ||||||
Components | Hypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region | ||||||
Keywords | OXIDOREDUCTASE / PhzF enzyme superfamily / double hot-dog / Structural Genomics / Paris-Sud Yeast Structural Genomics / YSG | ||||||
Function / homology | Function and homology information Isomerases; Racemases and epimerases / biosynthetic process / endoplasmic reticulum unfolded protein response / isomerase activity / chromatin / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.05 Å | ||||||
Authors | Liger, D. / Quevillon-Cheruel, S. / Sorel, I. / Bremang, M. / Blondeau, K. / Aboulfath, I. / Janin, J. / Van Tilbeurgh, H. / Leulliot, N. / Paris-Sud Yeast Structural Genomics (YSG) | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily Authors: Liger, D. / Quevillon-Cheruel, S. / Sorel, I. / Bremang, M. / Blondeau, K. / Aboulfath, I. / Janin, J. / van Tilbeurgh, H. / Leulliot, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ym5.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ym5.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ym5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ym5_validation.pdf.gz | 427.1 KB | Display | wwPDB validaton report |
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Full document | 1ym5_full_validation.pdf.gz | 430.6 KB | Display | |
Data in XML | 1ym5_validation.xml.gz | 14 KB | Display | |
Data in CIF | 1ym5_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/1ym5 ftp://data.pdbj.org/pub/pdb/validation_reports/ym/1ym5 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33427.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pet9 / Production host: Escherichia coli (E. coli) / References: UniProt: P38765 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 24% PEG 4000, 0.1M sodium acetate pH5, 0.2M ammonium acetate, 30% glycerol, 10mM DDT, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 2003 |
Radiation | Monochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→62.5 Å / Num. all: 21203 / Num. obs: 21044 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.043→2.096 Å / % possible all: 92.69 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.067 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0.4 / ESU R: 0.193 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 33.236 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.043→2.096 Å / Total num. of bins used: 20
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