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- PDB-3h8s: Structure of D19N T4 RNase H in the presence of divalent magnesium -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h8s | ||||||
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Title | Structure of D19N T4 RNase H in the presence of divalent magnesium | ||||||
![]() | Ribonuclease H | ||||||
![]() | HYDROLASE / BPT4 RNase H / 5'-3' exonuclease / Endonuclease / Nuclease | ||||||
Function / homology | ![]() DNA replication, Okazaki fragment processing / 5'-3' RNA exonuclease activity / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Tomanicek, S.J. / Mueser, T.C. | ||||||
![]() | ![]() Title: Additional Order Appears in the Absence of Metals in a FEN-1 protein: Structural Analysis of Magnesium Binding to Bacteriophage T4 RNaseH Authors: Tomanicek, S.J. / Devos, J.M. / Mueser, T.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73 KB | Display | ![]() |
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PDB format | ![]() | 52.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.8 KB | Display | ![]() |
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Full document | ![]() | 428.3 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3h7iC ![]() 3h8jC ![]() 3h8wC ![]() 1tfrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35609.926 Da / Num. of mol.: 1 / Mutation: D19N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM Na PIPES, 200 mM MgCl2, 14% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45 Å / Num. obs: 10519 / % possible obs: 83.1 % / Redundancy: 3 % / Biso Wilson estimate: 28.79 Å2 / Rmerge(I) obs: 0.035 / Χ2: 1.071 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 8.9 / Num. unique all: 679 / Χ2: 1.62 / % possible all: 55.2 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1TFR native T4 RNase H Resolution: 2.51→30.753 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.28 / σ(F): 2.59 / 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: 30.437 Å2 / ksol: 0.356 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.69 Å2 / Biso mean: 36.53 Å2 / Biso min: 10.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.51→30.753 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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