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Open data
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Basic information
Entry | Database: PDB / ID: 7vh4 | ||||||
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Title | Crystal structure of oligoribonuclease of Escherichia coli | ||||||
![]() | Oligoribonuclease | ||||||
![]() | HYDROLASE / Oligoribonuclease / ORN / RNase H-like fold / GENE REGULATION | ||||||
Function / homology | ACETATE ION / DI(HYDROXYETHYL)ETHER / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Badhwar, P. / Taneja, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Three-dimensional structure of a mycobacterial oligoribonuclease reveals a unique C-terminal tail that stabilizes the homodimer. Authors: Badhwar, P. / Khan, S.H. / Taneja, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160 KB | Display | ![]() |
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PDB format | ![]() | 125.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.7 KB | Display | ![]() |
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Full document | ![]() | 474.5 KB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 38.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wikC ![]() 2igiS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules DCBA
#1: Protein | Mass: 20927.680 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 190 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.26 % / Description: thin, flat, sheet-like |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20 mM Sodium HEPES, pH 7.5, 0.25 M Sodium acetate, 25 % v/v PEG-3350 PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI JUNGFRAU 4M / Detector: PIXEL / Date: May 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→59.63 Å / Num. obs: 34389 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 54.922 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.043 / Rrim(I) all: 0.086 / Χ2: 0.98 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 8 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3274 / Rpim(I) all: 0.299 / Rrim(I) all: 0.615 / % possible all: 98.6 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2IGI Resolution: 2.3→59.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.886 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.381 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 160.25 Å2 / Biso mean: 55.092 Å2 / Biso min: 26.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→59.63 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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