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Open data
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Basic information
Entry | Database: PDB / ID: 3ngy | ||||||
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Title | Crystal structure of RNase T (E92G mutant) | ||||||
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![]() | HYDROLASE / exoribonuclease / RNA processing / RNA maturation / protein-DNA interactions / exo-nuclease | ||||||
Function / homology | ![]() rRNA 3'-end processing / regulatory ncRNA 3'-end processing / tRNA 3'-end processing / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication proofreading / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / DNA damage response ...rRNA 3'-end processing / regulatory ncRNA 3'-end processing / tRNA 3'-end processing / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication proofreading / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / nucleic acid binding / DNA damage response / magnesium ion binding / protein homodimerization activity / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hsiao, Y.-Y. / Yuan, H.S. | ||||||
![]() | ![]() Title: Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation Authors: Hsiao, Y.-Y. / Yang, C.-C. / Lin, C.L. / Lin, J.L.J. / Duh, Y. / Yuan, H.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.6 KB | Display | ![]() |
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PDB format | ![]() | 134.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ngzC ![]() 3nh0C ![]() 3nh1C ![]() 3nh2C ![]() 2f96S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25646.973 Da / Num. of mol.: 4 / Mutation: E92G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P30014, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: Protein/peptide | | Mass: 795.827 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | CHAIN E IS THE N-TERMINAL HIS-TAG SEQUENCE OF ONE OF THE FOUR RNASE T SUBUNITS (CHAINS A-D). | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.0M ammonium citrate tribase pH 7.0, 0.1M BIS-TRIS propane pH 7.0, 10mM ErCl3-6H2O, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2008 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 39447 / Num. obs: 39447 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.058 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.9 / Num. unique all: 3547 / Rsym value: 0.3 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB 2F96 Resolution: 2.204→27.608 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8546 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.096 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.85 Å2 / Biso mean: 27.8473 Å2 / Biso min: 9.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.204→27.608 Å
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Refine LS restraints |
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LS refinement shell |
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