+Open data
-Basic information
Entry | Database: PDB / ID: 7vsa | |||||||||
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Title | E. coli Ribonuclease HI in complex with two Mg2+ | |||||||||
Components | Ribonuclease HI | |||||||||
Keywords | HYDROLASE / endonuclease / metalloenzyme | |||||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | |||||||||
Authors | Liao, Z. / Oyama, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vsa.cif.gz | 97.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vsa.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 7vsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/7vsa ftp://data.pdbj.org/pub/pdb/validation_reports/vs/7vsa | HTTPS FTP |
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-Related structure data
Related structure data | 7vsbC 7vscC 7vsdC 7vseC 4z0uS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.0483487524468, -0.998823420156, -0.00376476884243), (-0.998731339825, -0.0482904946908, -0.0142737161844), (0.0140751194678, 0.00445010900043, -0.999891037835)Vector: ...NCS oper: (Code: given Matrix: (0.0483487524468, -0.998823420156, -0.00376476884243), Vector: |
-Components
#1: Protein | Mass: 17622.998 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: rnhA, dasF, herA, rnh, sdrA, b0214, JW0204 / Production host: Escherichia coli (E. coli) / Strain (production host): MIC3001 / References: UniProt: P0A7Y4, ribonuclease H #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.26 Å3/Da / Density % sol: 45.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% w/v polyethylene glycol monomethyl ether 5,000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→48.89 Å / Num. obs: 32256 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 26.51 Å2 / CC1/2: 0.997 / CC star: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.038 / Rrim(I) all: 0.07 / Χ2: 1.03 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.76→1.79 Å / Rmerge(I) obs: 0.596 / Num. unique obs: 1799 / CC1/2: 0.913 / Rpim(I) all: 0.381 / Rrim(I) all: 0.706 / Χ2: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Z0U Resolution: 1.76→48.89 Å / SU ML: 0.216 / Cross valid method: FREE R-VALUE / σ(F): 0.37 / Phase error: 26.2021 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: 35.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→48.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.691980966854 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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