+Open data
-Basic information
Entry | Database: PDB / ID: 6hvl | ||||||
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Title | CdaA complex with c-di-AMP and AMP | ||||||
Components | Diadenylate cyclase | ||||||
Keywords | TRANSFERASE / di-adenylate cyclase / second messenger / complex / c-di-AMP / AMP | ||||||
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 serovar 1/2a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Heidemann, J.L. / Neumann, P. / Ficner, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Crystal structures of the c-di-AMP-synthesizing enzyme CdaA. Authors: Heidemann, J.L. / Neumann, P. / Dickmanns, A. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hvl.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hvl.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 6hvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hvl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6hvl_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6hvl_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 6hvl_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/6hvl ftp://data.pdbj.org/pub/pdb/validation_reports/hv/6hvl | HTTPS FTP |
-Related structure data
Related structure data | 6hvmC 6hvnC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 19369.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: dacA, cdaA, lmo2120 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Y5E4, diadenylate cyclase |
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-Non-polymers , 5 types, 10 molecules
#2: Chemical | ChemComp-2BA / ( |
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#3: Chemical | ChemComp-CO / |
#4: Chemical | ChemComp-PO4 / |
#5: Chemical | ChemComp-AMP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.79 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 m Ca(CH3OO)2, 0.1 M Na-HEPES pH 7.5, 10 % w/v PEG8000, |
-Data collection
Diffraction | Mean temperature: 180 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→42.271 Å / Num. obs: 9435 / % possible obs: 93.1 % / Redundancy: 5.649 % / Biso Wilson estimate: 57.26 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.118 / Χ2: 0.941 / Net I/σ(I): 12.39 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4rv7 Resolution: 2.8→42.271 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.51
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.02 Å2 / Biso mean: 57.9376 Å2 / Biso min: 23.42 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→42.271 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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