+Open data
-Basic information
Entry | Database: PDB / ID: 8c4q | |||||||||
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Title | CdaA-Apo | |||||||||
Components | Diadenylate cyclase | |||||||||
Keywords | PROTEIN BINDING / Complex | |||||||||
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 | Listeria monocytogenes (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å | |||||||||
Authors | Neumann, P. / Ficner, R. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Microlife / Year: 2023 Title: Computer-aided design of a cyclic di-AMP synthesizing enzyme CdaA inhibitor. Authors: Neumann, P. / Kloskowski, 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 | 8c4q.cif.gz | 168 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c4q.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 8c4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c4q_validation.pdf.gz | 433.2 KB | Display | wwPDB validaton report |
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Full document | 8c4q_full_validation.pdf.gz | 436.2 KB | Display | |
Data in XML | 8c4q_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 8c4q_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/8c4q ftp://data.pdbj.org/pub/pdb/validation_reports/c4/8c4q | HTTPS FTP |
-Related structure data
Related structure data | 8c4jC 8c4mC 8c4nC 8c4oC 8c4pC 8c4rC C: citing same article (ref.) |
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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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19369.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: dacA, cdaA, lmo2120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y5E4, diadenylate cyclase #2: Chemical | ChemComp-CL / #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: 2.3 Å3/Da / Density % sol: 46.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 3.7 M NaCl, 0.1M Na-HEPES pH 8.5 and 3 % DMSO |
-Data collection
Diffraction | Mean temperature: 180 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.6888 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.6888 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.38→50 Å / Num. obs: 72378 / % possible obs: 97.1 % / Redundancy: 8 % / Biso Wilson estimate: 26.94 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.05 / Net I/σ(I): 18.63 | ||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→35.87 Å / SU ML: 0.2123 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.5912 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→35.87 Å
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Refine LS restraints |
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LS refinement shell |
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