+Open data
-Basic information
Entry | Database: PDB / ID: 9do4 | ||||||
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Title | Structure of T4 RNA Ligase 1 bound to ATP and Mg | ||||||
Components | RNA ligase 1 | ||||||
Keywords | LIGASE / T4 RNA ligase 1 | ||||||
Function / homology | Function and homology information virus tail fiber assembly / RNA ligase (ATP) / RNA ligase (ATP) activity / RNA repair / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Wimberly-Gard, G.M. / Shuman, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure of T4 RNA Ligase 1 bound to ATP and Mg Authors: Wimberly-Gard, G.M. / Shuman, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9do4.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9do4.ent.gz | 61.5 KB | Display | PDB format |
PDBx/mmJSON format | 9do4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9do4_validation.pdf.gz | 788.1 KB | Display | wwPDB validaton report |
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Full document | 9do4_full_validation.pdf.gz | 790.3 KB | Display | |
Data in XML | 9do4_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 9do4_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/9do4 ftp://data.pdbj.org/pub/pdb/validation_reports/do/9do4 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46095.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 63 / Production host: Escherichia coli (E. coli) / References: UniProt: P00971, RNA ligase (ATP) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ATP / | #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: 2.17 Å3/Da / Density % sol: 43.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 300mM MGCl2, 100mM NaCl, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 13, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.920105 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 12514 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 52.403 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.099 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.6→2.72 Å / Rmerge(I) obs: 1.588 / Num. unique obs: 1511 / CC1/2: 0.381 / Rpim(I) all: 0.824 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→27.83 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→27.83 Å
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Refine LS restraints |
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LS refinement shell |
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