+Open data
-Basic information
Entry | Database: PDB / ID: 7l8n | |||||||||
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Title | Diadenylate cyclase with AMP from Streptococcus mutans | |||||||||
Components | Diadenylate cyclase | |||||||||
Keywords | TRANSFERASE / cyclase / ATP / AMP / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | Function and homology information diadenylate cyclase / : / cAMP biosynthetic process / adenylate cyclase activity / nucleotidyltransferase activity / membrane => GO:0016020 / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Streptococcus mutans serotype c (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | |||||||||
Authors | Hua, Z. / Hui, W. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Diadenylate cyclase with AMP from Streptococcus mutans Authors: Hua, Z. / Hui, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l8n.cif.gz | 154.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l8n.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 7l8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/7l8n ftp://data.pdbj.org/pub/pdb/validation_reports/l8/7l8n | HTTPS FTP |
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-Related structure data
Related structure data | 4rv7S S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 16408.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans serotype c (strain ATCC 700610 / UA159) (bacteria) Strain: ATCC 700610 / UA159 / Gene: dacA, SMU_1428c / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8DTC4, diadenylate cyclase |
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-Non-polymers , 5 types, 202 molecules
#2: Chemical | ChemComp-AMP / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-MLI / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
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: 2.48 Å3/Da / Density % sol: 50.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1M sodium malonate pH 5.0, 0.1M sodium acetate trihydrate pH 4.5, 2% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→100 Å / Num. obs: 24283 / % possible obs: 99.8 % / Redundancy: 13.79 % / Biso Wilson estimate: 26.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.46 |
Reflection shell | Resolution: 1.94→1.98 Å / Num. unique obs: 8160 / CC1/2: 0.945 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4rv7 Resolution: 1.94→38.97 Å / SU ML: 0.1787 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 19.5258 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 33.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→38.97 Å
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Refine LS restraints |
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LS refinement shell |
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