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Yorodumi- PDB-1yhf: Crystal Structure of Conserved SPY1581 Protein of Unknown Functio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yhf | ||||||
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Title | Crystal Structure of Conserved SPY1581 Protein of Unknown Function from Streptococcus pyogenes | ||||||
Components | hypothetical protein SPy1581 | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Osipiuk, J. / Lezondra, L. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yhf.cif.gz | 33.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yhf.ent.gz | 25.8 KB | Display | PDB format |
PDBx/mmJSON format | 1yhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yhf_validation.pdf.gz | 415.2 KB | Display | wwPDB validaton report |
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Full document | 1yhf_full_validation.pdf.gz | 415.9 KB | Display | |
Data in XML | 1yhf_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 1yhf_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/1yhf ftp://data.pdbj.org/pub/pdb/validation_reports/yh/1yhf | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-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.) Streptococcus pyogenes (bacteria) / Strain: M1 GAS / Gene: SPy1581 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99YR1 |
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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: 2.3 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: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97946 |
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: SAD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→39.9 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 5.982 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / ESU R: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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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