+Open data
-Basic information
Entry | Database: PDB / ID: 6yj9 | ||||||
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Title | DarB in complex with 3'3'cGAMP | ||||||
Components | CBS domain-containing protein YkuL | ||||||
Keywords | UNKNOWN FUNCTION / c-di-AMP binding protein | ||||||
Function / homology | : / CBS domain superfamily / Chem-4BW / Cyclic di-AMP receptor B Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Heidemann, J.L. / Neumann, P. / Ficner, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: DarB from B. subtilis Authors: Heidemann, J.L. / Neumann, P. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yj9.cif.gz | 144.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yj9.ent.gz | 112 KB | Display | PDB format |
PDBx/mmJSON format | 6yj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/6yj9 ftp://data.pdbj.org/pub/pdb/validation_reports/yj/6yj9 | HTTPS FTP |
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-Related structure data
Related structure data | 6yj7C 6yj8C 6yjaC 1yavS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16653.346 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Gene: ykuL, BSU14130 / Production host: Escherichia coli (E. coli) / References: UniProt: O31698 #2: Chemical | ChemComp-4BW / #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Has ligand of interest | 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: 2.3 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris/HCl PH 8.5, 32 % w/v polyethylene glycol 4000, 5 % v/v/ glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→35.68 Å / Num. obs: 50229 / % possible obs: 99.9 % / Redundancy: 12.958 % / Biso Wilson estimate: 30.806 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.039 / Χ2: 1.043 / Net I/σ(I): 31.06 / Num. measured all: 650885 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YAV Resolution: 1.5→35.68 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.65 / 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: 82.87 Å2 / Biso mean: 31.4686 Å2 / Biso min: 16.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→35.68 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18
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