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- PDB-7vsb: E. coli Ribonuclease HI in complex with one Zn2+ (His124 N-delta ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vsb | |||||||||
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Title | E. coli Ribonuclease HI in complex with one Zn2+ (His124 N-delta binding) | |||||||||
![]() | Ribonuclease HI | |||||||||
![]() | HYDROLASE / endonuclease / metalloenzyme | |||||||||
Function / homology | ![]() DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / endonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Liao, Z. / Oyama, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography. Authors: Liao, Z. / Oyama, T. / Kitagawa, Y. / Katayanagi, K. / Morikawa, K. / Oda, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.3 KB | Display | ![]() |
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PDB format | ![]() | 57.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7vsaC ![]() 7vscC ![]() 7vsdC ![]() 7vseC ![]() 4z0uS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17622.998 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: rnhA, dasF, herA, rnh, sdrA, b0214, JW0204 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M sodium citrate tribasic dihydrate pH 5.6, 20% v/v 2-propanol, 20% w/v polyethylene glycol 4,000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→48.5 Å / Num. obs: 26808 / % possible obs: 99.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 21.06 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.041 / Rrim(I) all: 0.102 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.84→1.88 Å / Rmerge(I) obs: 0.384 / Num. unique obs: 1623 / CC1/2: 0.991 / Rpim(I) all: 0.179 / Rrim(I) all: 0.424 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4z0u Resolution: 1.84→48.5 Å / SU ML: 0.1998 / Cross valid method: FREE R-VALUE / σ(F): 0.77 / Phase error: 21.6046 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→48.5 Å
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Refine LS restraints |
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LS refinement shell |
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