[English] 日本語
Yorodumi- PDB-7dfx: Structure and function of Diadenylate cyclase DacM in Mycoplasma ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dfx | ||||||
---|---|---|---|---|---|---|---|
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 | DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily / DisA bacterial checkpoint controller nucleotide-binding / Diadenylate cyclase (DAC) domain profile. / diadenylate cyclase activity / membrane => GO:0016020 / ATP binding / MALONIC ACID / DAC domain-containing protein Function and homology information | ||||||
Biological species | Mycoplasma ovipneumoniae 14811 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.996 Å | ||||||
Authors | Fan, S. / Li, M. | ||||||
Citation | Journal: To Be Published Title: Structure and function of Diadenylate cyclase DacM in Mycoplasma ovipneumoniae Authors: Li, M. / Fan, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7dfx.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7dfx.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 7dfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dfx_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7dfx_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7dfx_validation.xml.gz | 15 KB | Display | |
Data in CIF | 7dfx_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/7dfx ftp://data.pdbj.org/pub/pdb/validation_reports/df/7dfx | HTTPS FTP |
-Related structure data
Related structure data | 7dg0C 4rv7S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 19507.145 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-MLA / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 7.54 Å3/Da / Density % sol: 83.69 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 1 M sodium malonate pH 5.0, 0.1 M citric acid pH 3.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 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: 2.99→50 Å / Num. obs: 23720 / % possible obs: 100 % / Redundancy: 36.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.208 / Net I/σ(I): 23 |
Reflection shell | Resolution: 3→50 Å / Rmerge(I) obs: 0.208 / Num. unique obs: 23720 / CC1/2: 0.361 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4rv7 Resolution: 2.996→32.941 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.43 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.79 Å2 / Biso mean: 54.4221 Å2 / Biso min: 18.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.996→32.941 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|