+Open data
-Basic information
Entry | Database: PDB / ID: 4qak | ||||||
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Title | Crystal structure of phosphoesterase | ||||||
Components | 2'-5'-RNA ligase | ||||||
Keywords | HYDROLASE / RNA 2' / 3' cyclic phosphodiesterase / 2H motif / phosphodiesterase / RNA | ||||||
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 Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.025 Å | ||||||
Authors | Remus, B.S. / Shuman, S. | ||||||
Citation | Journal: To be Published Title: Structure of phosphoesterase Authors: Remus, B.S. / Shuman, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qak.cif.gz | 156.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qak.ent.gz | 131.3 KB | Display | PDB format |
PDBx/mmJSON format | 4qak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qak_validation.pdf.gz | 848.8 KB | Display | wwPDB validaton report |
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Full document | 4qak_full_validation.pdf.gz | 849.1 KB | Display | |
Data in XML | 4qak_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 4qak_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/4qak ftp://data.pdbj.org/pub/pdb/validation_reports/qa/4qak | HTTPS FTP |
-Related structure data
Similar structure data |
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-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20187.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 References: UniProt: P37025, Ligases; Forming phosphoric-ester bonds #2: Chemical | #3: Chemical | ChemComp-2AM / | #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: 2.57 Å3/Da / Density % sol: 52.19 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 2M NaCl, 0.1mM sodium acetate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2014 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→48.16 Å / Num. all: 28005 / Num. obs: 27221 / % possible obs: 97.2 % / Observed criterion σ(F): 0.007 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 2.02→2.1 Å / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.025→48.16 Å / SU ML: 0.23 / σ(F): 1.36 / Phase error: 22.73 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.025→48.16 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 28.1224 Å / Origin y: 28.1529 Å / Origin z: 17.2253 Å
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Refinement TLS group | Selection details: all |