+Open data
-Basic information
Entry | Database: PDB / ID: 5xt3 | ||||||
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Title | The catalytic domain of GdpP with c-di-GMP | ||||||
Components | Phosphodiesterase acting on cyclic dinucleotides | ||||||
Keywords | HYDROLASE / phosphodiesterase | ||||||
Function / homology | Function and homology information cyclic-di-AMP phosphodiesterase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / nucleic acid binding / hydrolase activity / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.591 Å | ||||||
Authors | Wang, F. / Gu, L. | ||||||
Citation | Journal: Biochem. J. / Year: 2018 Title: Structural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase Authors: Wang, F. / He, Q. / Su, K. / Wei, T. / Xu, S. / Gu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xt3.cif.gz | 148.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xt3.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xt3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/5xt3 ftp://data.pdbj.org/pub/pdb/validation_reports/xt/5xt3 | HTTPS FTP |
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-Related structure data
Related structure data | 5xsiSC 5xsnC 5xspC 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
#1: Protein | Mass: 37728.801 Da / Num. of mol.: 2 / Fragment: UNP residues 32-657 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cdnD, BN1321_430104 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0U1MUE2 #2: Chemical | #3: Chemical | #4: 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: 2.74 Å3/Da / Density % sol: 55.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10% (w/v) PEG8000, 0.1 M imidazole pH 7.5, 0.2 M calcium acetate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 26562 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 24.44 |
Reflection shell | Resolution: 2.6→43.5 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.438 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XSI Resolution: 2.591→43.514 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.941 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.591→43.514 Å
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Refine LS restraints |
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LS refinement shell |
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