+Open data
-Basic information
Entry | Database: PDB / ID: 5ldk | ||||||
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Title | Crystal structure of E.coli LigT complexed with ATP | ||||||
Components | RNA 2',3'-cyclic phosphodiesterase | ||||||
Keywords | HYDROLASE / Enzyme / 2H phosphoesterase/ligase | ||||||
Function / homology | Function and homology information RNA 2',3'-cyclic 3'-phosphodiesterase / RNA 2',3'-cyclic 3'-phosphodiesterase activity / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å | ||||||
Authors | Myllykoski, M. / Kursula, P. | ||||||
Citation | Journal: PLoS ONE / Year: 2017 Title: Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase. Authors: Myllykoski, M. / Kursula, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ldk.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ldk.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ldk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ldk_validation.pdf.gz | 870.8 KB | Display | wwPDB validaton report |
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Full document | 5ldk_full_validation.pdf.gz | 875.9 KB | Display | |
Data in XML | 5ldk_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 5ldk_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/5ldk ftp://data.pdbj.org/pub/pdb/validation_reports/ld/5ldk | HTTPS FTP |
-Related structure data
Related structure data | 5ldiSC 5ldjC 5ldmC 5ldoC 5ldpC 5ldqC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20045.029 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain B / BL21-DE3) (bacteria) Gene: thpR, ECBD_3472 / Plasmid: pTH 27 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A140NFI1, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases #2: Chemical | ChemComp-ATP / | #3: Water | ChemComp-HOH / | |
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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: 2.83 Å3/Da / Density % sol: 56.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Tris-HCl pH 7.5, 0.2 M MgCl2, 18% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→30 Å / Num. obs: 26124 / % possible obs: 99.2 % / Redundancy: 3.81 % / Biso Wilson estimate: 32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.16 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 1.65 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDBid: 5ldi Resolution: 2.099→23.37 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 24.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.099→23.37 Å
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Refine LS restraints |
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LS refinement shell |
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