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Yorodumi- PDB-8ohb: PanDDA analysis group deposition -- CdaA in complex with fragment... -
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-Basic information
Entry | Database: PDB / ID: 8ohb | ||||||
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Title | PanDDA analysis group deposition -- CdaA in complex with fragment F2X-Entry E08 | ||||||
Components | Cyclic di-AMP synthase CdaA | ||||||
Keywords | TRANSFERASE / diadenylate cyclase | ||||||
Function / homology | Function and homology information diadenylate cyclase activity / diadenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å | ||||||
Authors | Garbers, T.B. / Neumann, P. / Wollenhaupt, J. / Weiss, M.S. / Ficner, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: PanDDA analysis group deposition -- CdaA in complex with fragment F2X-Entry E08 Authors: Garbers, T.B. / Neumann, P. / Wollenhaupt, J. / Weiss, M.S. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ohb.cif.gz | 209.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ohb.ent.gz | 146.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ohb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ohb_validation.pdf.gz | 834.4 KB | Display | wwPDB validaton report |
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Full document | 8ohb_full_validation.pdf.gz | 835.2 KB | Display | |
Data in XML | 8ohb_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 8ohb_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/8ohb ftp://data.pdbj.org/pub/pdb/validation_reports/oh/8ohb | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16681.018 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: cdaA, ybbP, BSU01750 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q45589, diadenylate cyclase #2: Chemical | ChemComp-UHL / | Mass: 143.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9N3O2 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-MG / | #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: 2.36 Å3/Da / Density % sol: 47.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5 0.1 M Magnesium chloride 30 % (v/v) PEG 400 20 % (v/v) DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 6, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.11→50 Å / Num. obs: 202832 / % possible obs: 93.5 % / Redundancy: 2.5 % / Biso Wilson estimate: 15.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.072 / Net I/σ(I): 7.06 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.11→42.69 Å / SU ML: 0.1838 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2691 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.11→42.69 Å
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Refine LS restraints |
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LS refinement shell |
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