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- PDB-3h8w: Structure of D132N 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: 3h8w | ||||||
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Title | Structure of D132N 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 | ![]() | 69.5 KB | Display | ![]() |
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PDB format | ![]() | 50.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.1 KB | Display | ![]() |
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Full document | ![]() | 429.7 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 15.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3h7iC ![]() 3h8jC ![]() 3h8sC ![]() 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: D132N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.35 % |
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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: 2.8→34.34 Å / Num. obs: 8890 / % possible obs: 97.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 4.3 / Num. measured all: 4280 / Num. unique all: 1242 / Rsym value: 0.177 / % possible all: 94.5 |
-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: 2.8→34.34 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.48 / σ(F): 1.35 / 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: 35.949 Å2 / ksol: 0.315 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.25 Å2 / Biso mean: 44.94 Å2 / Biso min: 48.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→34.34 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: 6
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