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Yorodumi- PDB-3nh1: Crystal structure of RNase T in complex with a preferred ssDNA (T... -
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-Basic information
Entry | Database: PDB / ID: 3nh1 | ||||||
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Title | Crystal structure of RNase T in complex with a preferred ssDNA (TAGG) with two Mg in the active site | ||||||
Components |
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Keywords | HYDROLASE/DNA / exoribonuclease / RNA processing / RNA maturation / protein-DNA interactions / protein-DNA complex / exo-nuclease / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information rRNA 3'-end processing / tRNA 3'-end processing / regulatory ncRNA 3'-end processing / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / 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 / tRNA 3'-end processing / regulatory ncRNA 3'-end processing / DNA replication proofreading / single-stranded DNA 3'-5' DNA exonuclease activity / 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.107 Å | ||||||
Authors | Hsiao, Y.-Y. / Yuan, H.S. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nh1.cif.gz | 188.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nh1.ent.gz | 146.2 KB | Display | PDB format |
PDBx/mmJSON format | 3nh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nh/3nh1 ftp://data.pdbj.org/pub/pdb/validation_reports/nh/3nh1 | HTTPS FTP |
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-Related structure data
Related structure data | 3ngySC 3ngzC 3nh0C 3nh2C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25719.035 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / ATCC 53323 / Gene: rnt / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): RIPL References: UniProt: P30014, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters #2: DNA chain | Mass: 2152.446 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: ssDNA #3: Chemical | ChemComp-MG / #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: 1.767152 Å3/Da / Density % sol: 30.396488 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M MES monohydrate pH 6.0, 20% w/v PEG MME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.999 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2010 |
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: 2.1→30 Å / Num. all: 43799 / Num. obs: 43799 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.056 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 4281 / Rsym value: 0.269 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NGY Resolution: 2.107→23.377 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.851 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 22.87 / 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: 36.878 Å2 / ksol: 0.358 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.58 Å2 / Biso mean: 31.0035 Å2 / Biso min: 11.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2.107→23.377 Å
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Refine LS restraints |
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LS refinement shell |
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