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Yorodumi- PDB-3omt: Putative antitoxin component, CHU_2935 protein, from Xre family f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3omt | ||||||
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Title | Putative antitoxin component, CHU_2935 protein, from Xre family from Prevotella buccae. | ||||||
Components | uncharacterized protein | ||||||
Keywords | structural genomics / unknown function / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / toxin-antitoxin system / antitoxin component / Xre family | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cytophaga hutchinsonii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Osipiuk, J. / Bigelow, L. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of putative antitoxin component, CHU_2935 protein, from Xre family from Prevotella buccae. Authors: Osipiuk, J. / Bigelow, L. / Abdullah, J. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3omt.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3omt.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 3omt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3omt_validation.pdf.gz | 427.9 KB | Display | wwPDB validaton report |
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Full document | 3omt_full_validation.pdf.gz | 428.7 KB | Display | |
Data in XML | 3omt_validation.xml.gz | 10 KB | Display | |
Data in CIF | 3omt_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/3omt ftp://data.pdbj.org/pub/pdb/validation_reports/om/3omt | HTTPS FTP |
-Related structure data
Related structure data | 3bs3S S: Starting model for refinement |
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Similar structure data | |
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: 8365.593 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / Gene: CHU_2935 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q11QY7 #2: Chemical | ChemComp-PO4 / | #3: Water | ChemComp-HOH / | |
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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: 2.31 Å3/Da / Density % sol: 46.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 2 M ammonium sulfate, 0.1 M phosphate citrate-buffer, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→39.8 Å / Num. all: 19302 / Num. obs: 19302 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.098 / Χ2: 1.223 / Net I/σ(I): 7.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BS3 Resolution: 1.65→39.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.183 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.79 Å2 / Biso mean: 16.7633 Å2 / Biso min: 5.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→39.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.651→1.694 Å / Total num. of bins used: 20
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