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Open data
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Basic information
Entry | Database: PDB / ID: 3h8j | ||||||
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Title | Native T4 RNase H in the absence of divalent metal ions | ||||||
![]() | 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 | ![]() | 80.4 KB | Display | ![]() |
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PDB format | ![]() | 58.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.2 KB | Display | ![]() |
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Full document | ![]() | 436 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3h7iC ![]() 3h8sC ![]() 3h8wC ![]() 1tfrS 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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Unit cell |
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Components
#1: Protein | Mass: 35610.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.62 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 300 mM ammonium acetate, 100 mM sodium cacodylate, 15% 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 | Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 33128 / Redundancy: 4 % / Biso Wilson estimate: 15.47 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 7.4 / Num. unique all: 3285 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1TFR native T4 RNase H Resolution: 1.8→19.253 Å / SU ML: 0.23 / σ(F): 0.05 / 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: 36.403 Å2 / ksol: 0.388 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.253 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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