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- PDB-1ct5: CRYSTAL STRUCTURE OF YEAST HYPOTHETICAL PROTEIN YBL036C-SELENOMET... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ct5 | ||||||
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Title | CRYSTAL STRUCTURE OF YEAST HYPOTHETICAL PROTEIN YBL036C-SELENOMET CRYSTAL | ||||||
![]() | PROTEIN (YEAST HYPOTHETICAL PROTEIN, SELENOMET) | ||||||
![]() | STRUCTURAL GENOMICS / TIM BARREL / YEAST / PYRIDOXAL-5'-PHOSPHATE / SELENOMETHIONINE / MAD / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | ![]() vitamin B6 metabolic process / pyridoxal phosphate binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Eswaramoorthy, S. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Structure of a yeast hypothetical protein selected by a structural genomics approach. Authors: Eswaramoorthy, S. / Gerchman, S. / Graziano, V. / Kycia, H. / Studier, F.W. / Swaminathan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.2 KB | Display | ![]() |
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PDB format | ![]() | 46.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29173.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: YBL 036C / Plasmid: PET-13A B834(DE3) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-PLP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 0.5 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate, 2.9 mg/ml protein in 6.25mM HEPES and 62.5mM NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.6 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS / Detector: CCD / Date: Nov 12, 1998 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9803 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 20510 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.253 / % possible all: 94.9 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Num. measured all: 138645 / Biso Wilson estimate: 19 Å2 |
Reflection shell | *PLUS % possible obs: 94.9 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2→12.5 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12.5 Å / Rfactor obs: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |