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- PDB-1yhf: Crystal Structure of Conserved SPY1581 Protein of Unknown Functio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yhf | ||||||
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Title | Crystal Structure of Conserved SPY1581 Protein of Unknown Function from Streptococcus pyogenes | ||||||
![]() | hypothetical protein SPy1581 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Cupin_2 domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Osipiuk, J. / Lezondra, L. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: X-ray crystal structure of conserved hypothetical SPy1581 protein from Streptococcus pyogenes. Authors: Osipiuk, J. / Lezondra, L. / Moy, S. / Collart, F. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.8 KB | Display | ![]() |
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PDB format | ![]() | 25.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.2 KB | Display | ![]() |
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Full document | ![]() | 415.9 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 10.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 12931.826 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.6 % |
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Crystal grow | Temperature: 293 K / pH: 4.5 Details: 30% PEG 3000, 0.1 M Sodium Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 4.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-3 / Detector: CCD / Date: Dec 2, 2004 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 8535 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 23.4 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 33.6 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 2.62 / % possible all: 94.8 |
-Phasing
Phasing | Method: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm shell |
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Processing
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Refinement | Method to determine structure: ![]() Details: ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R- FACTORS, R-WORK AND R-FREE, ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2→39.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 22.7025 Å / Origin y: 14.9165 Å / Origin z: 27.3086 Å
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