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Yorodumi- PDB-7k9c: Crystal structure of Bacillus halodurans OapB (iodine-derivative)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k9c | |||||||||
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Title | Crystal structure of Bacillus halodurans OapB (iodine-derivative) at 1.0 A | |||||||||
Components | OLE-associated protein B | |||||||||
Keywords | RNA / ribonucleoprotein complex / OLE RNA / RNA BINDING PROTEIN | |||||||||
Function / homology | Ribosomal protein L14, KOW motif / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / IODIDE ION / BH0157 protein Function and homology information | |||||||||
Biological species | Bacillus halodurans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1 Å | |||||||||
Authors | Yang, Y. / Breaker, R.R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex. Authors: Yang, Y. / Harris, K.A. / Widner, D.L. / Breaker, R.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7k9c.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k9c.ent.gz | 119.6 KB | Display | PDB format |
PDBx/mmJSON format | 7k9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k9c_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 7k9c_full_validation.pdf.gz | 426.3 KB | Display | |
Data in XML | 7k9c_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 7k9c_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/7k9c ftp://data.pdbj.org/pub/pdb/validation_reports/k9/7k9c | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11378.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125) (bacteria) Strain: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125 Gene: BH0157 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KGD7 #2: Chemical | ChemComp-IOD / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.82 Å3/Da / Density % sol: 32.56 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 50 mM Tris-HCl (pH 8.5), 100 mM KCl, 10 mM MgCl2 and 30% polyethylene glycol (PEG) 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.8266 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 1→49.7 Å / Num. obs: 85634 / % possible obs: 96.4 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.033 / Rrim(I) all: 0.069 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 4 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8108 / CC1/2: 0.573 / Rpim(I) all: 0.519 / Rrim(I) all: 1.072 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1→49.637 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.42 / 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: 49.09 Å2 / Biso mean: 15.4759 Å2 / Biso min: 6.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1→49.637 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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