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Yorodumi- PDB-7dg0: Structure and function of Diadenylate cyclase DacM in Mycoplasma ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dg0 | ||||||
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Title | Structure and function of Diadenylate cyclase DacM in Mycoplasma ovipneumoniae | ||||||
Components | DAC domain-containing protein | ||||||
Keywords | IMMUNE SYSTEM / second messenger / c-di-AMP / diadenylate cyclase / Mycoplasma ovipneumoniae | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycoplasma ovipneumoniae 14811 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.895 Å | ||||||
Authors | Fan, S.L. | ||||||
Citation | Journal: To Be Published Title: Structure and function of Diadenylate cyclase DacM in Mycoplasma ovipneumoniae Authors: Li, M. / Fan, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dg0.cif.gz | 152 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dg0.ent.gz | 117.5 KB | Display | PDB format |
PDBx/mmJSON format | 7dg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dg0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7dg0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7dg0_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 7dg0_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dg/7dg0 ftp://data.pdbj.org/pub/pdb/validation_reports/dg/7dg0 | HTTPS FTP |
-Related structure data
Related structure data | 7dfxC 4rv7S 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: 19645.291 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma ovipneumoniae 14811 (bacteria) Gene: MOVI_0530 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: A0A014M399 #2: Chemical | ChemComp-ATP / | #3: Chemical | ChemComp-ADP / | #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: 2.03 Å3/Da / Density % sol: 39.52 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 19% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→50 Å / Num. obs: 24587 / % possible obs: 99.9 % / Redundancy: 12.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 1.89→1.97 Å / Rmerge(I) obs: 0.084 / Num. unique obs: 24587 / CC1/2: 0.995 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RV7 Resolution: 1.895→26.196 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.69 / 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: 102.01 Å2 / Biso mean: 28.7619 Å2 / Biso min: 5.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.895→26.196 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -16.0478 Å / Origin y: -1.597 Å / Origin z: 17.8892 Å
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Refinement TLS group | Selection details: all |