+Open data
-Basic information
Entry | Database: PDB / ID: 7d4j | ||||||
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Title | ddATP complex of cyclic trinucleotide synthase CdnD | ||||||
Components | Cyclic AMP-AMP-GMP synthase | ||||||
Keywords | TRANSFERASE / substrate analogue dideoxy adenosine triphosphate cyclic trinucleotide synthesis nucleotidyl transferase | ||||||
Function / homology | Function and homology information nucleotide metabolic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / GTP binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Yang, C.-S. / Hou, M.-H. / Tsai, C.-L. / Wang, Y.-C. / Ko, T.-P. / Chen, Y. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Crystal structure and functional implication of a bacterial cyclic AMP-AMP-GMP synthetase. Authors: Ko, T.P. / Wang, Y.C. / Tsai, C.L. / Yang, C.S. / Hou, M.H. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d4j.cif.gz | 164.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d4j.ent.gz | 127.5 KB | Display | PDB format |
PDBx/mmJSON format | 7d4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/7d4j ftp://data.pdbj.org/pub/pdb/validation_reports/d4/7d4j | HTTPS FTP |
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-Related structure data
Related structure data | 7d48SC 7d4oC 7d4sC 7d4uC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 44378.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: cdnD02, P853_02262 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0DSP4, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases | ||||
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#2: Chemical | ChemComp-DDS / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 2 mM ddATP, 10 mM GTP, 10 mM MgCl2, 0.2 M ammonium tartrate dibasic, pH 7.0, 26% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9998 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 30653 / % possible obs: 99.1 % / Redundancy: 9.7 % / Biso Wilson estimate: 24.14 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2.09→2.16 Å / Redundancy: 5 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.4 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 7D48 Resolution: 2.09→28.37 Å / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.305 / Stereochemistry target values: GEOSTD + MONOMER LIBRARY
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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: 30.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→28.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.17 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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