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Yorodumi- PDB-7f25: Crystal structure of SSB from Salmonella enterica serovar Typhimu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f25 | ||||||
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Title | Crystal structure of SSB from Salmonella enterica serovar Typhimurium LT2. | ||||||
Components | Single-stranded DNA-binding protein 1 | ||||||
Keywords | DNA BINDING PROTEIN / Single-stranded DNA-binding protein / SSB | ||||||
Function / homology | Function and homology information positive regulation of helicase activity / nucleoid / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å | ||||||
Authors | Luo, R.H. / Huang, Y.H. / Huang, C.Y. | ||||||
Funding support | 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Crystal Structure of an SSB Protein from Salmonella enterica and Its Inhibition by Flavanonol Taxifolin. Authors: Lin, E.S. / Huang, Y.H. / Luo, R.H. / Basharat, Z. / Huang, C.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f25.cif.gz | 55.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f25.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7f25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/7f25 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/7f25 | HTTPS FTP |
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-Related structure data
Related structure data | 1eygS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 13762.536 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Gene: ssb, STM4256 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A2F6 #2: 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: 2.7 Å3/Da / Density % sol: 54.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 15% PEG 400, 100mM sodium Salt, pH6.5 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→30 Å / Num. obs: 7050 / % possible obs: 99.9 % / Redundancy: 5.3 % / CC1/2: 0.792 / Net I/σ(I): 20.34 |
Reflection shell | Resolution: 2.87→2.97 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.31 / Num. unique obs: 691 / CC1/2: 0.918 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EYG Resolution: 2.87→28.5 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 37.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.48 Å2 / Biso mean: 66.1348 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.87→28.5 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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