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Yorodumi- PDB-2oqt: Structural Genomics, the crystal structure of a putative PTS IIA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oqt | ||||||
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Title | Structural Genomics, the crystal structure of a putative PTS IIA domain from Streptococcus pyogenes M1 GAS | ||||||
Components | Hypothetical protein SPy0176 | ||||||
Keywords | TRANSFERASE / APC29699 / putative PTS IIA domain / Streptococcus pyogenes M1 GAS / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG | ||||||
Function / homology | PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / PTS_EIIA type-2 domain profile. / Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Phosphotransferase/anion transporter / 3-Layer(aba) Sandwich / Alpha Beta / PTS EIIA type-2 domain-containing protein Function and homology information | ||||||
Biological species | Streptococcus pyogenes serotype M1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.41 Å | ||||||
Authors | Tan, K. / Wu, R. / Osipiuk, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a putative PTS IIA domain from Streptococcus pyogenes M1 GAS Authors: Tan, K. / Wu, R. / Osipiuk, J. / Clancy, S. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ... BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS A MONOMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). | ||||||
Remark 999 | SEQUENCE AUTHORS STATE THAT THERE IS A MUTATION F7L FROM UNKNOWN SOURCE IN COMPARISON TO THE ... SEQUENCE AUTHORS STATE THAT THERE IS A MUTATION F7L FROM UNKNOWN SOURCE IN COMPARISON TO THE DATABASE SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oqt.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oqt.ent.gz | 100.7 KB | Display | PDB format |
PDBx/mmJSON format | 2oqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oqt_validation.pdf.gz | 461 KB | Display | wwPDB validaton report |
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Full document | 2oqt_full_validation.pdf.gz | 485.4 KB | Display | |
Data in XML | 2oqt_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 2oqt_validation.cif.gz | 33.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/2oqt ftp://data.pdbj.org/pub/pdb/validation_reports/oq/2oqt | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 17806.418 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria) Species: Streptococcus pyogenes / Strain: M1 GAS, SF370 / Gene: SPy0176 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9A1N7 #2: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.42 Å3/Da / Density % sol: 49.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 20% PEG3350, 0.2M Li2SO4, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924, 0.97938 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2006 / Details: mirror | |||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→35.85 Å / Num. all: 23714 / Num. obs: 23714 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 34.86 | |||||||||
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 5 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.02 / Num. unique all: 912 / % possible all: 52.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.41→35.85 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 21.172 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.593 / ESU R Free: 0.295 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.214 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→35.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.47 Å / Total num. of bins used: 20
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