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- PDB-8oqf: Cross-linked crystal of Dirhodium tetraacetate/ribonuclease A add... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8oqf | |||||||||||||||
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Title | Cross-linked crystal of Dirhodium tetraacetate/ribonuclease A adduct in the P3221 space group (low temperature data collection) | |||||||||||||||
![]() | Ribonuclease pancreatic | |||||||||||||||
![]() | HYDROLASE / Metal/protein adduct / dirhodium tetraacettate / catalysis / porous material | |||||||||||||||
Function / homology | ![]() pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Loreto, D. / Merlino, A. / Maity, B. / Ueno, T. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Cross-Linked Crystals of Dirhodium Tetraacetate/RNase A Adduct Can Be Used as Heterogeneous Catalysts. Authors: Loreto, D. / Maity, B. / Morita, T. / Nakamura, H. / Merlino, A. / Ueno, T. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 46.3 KB | Display | ![]() |
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PDB format | ![]() | 32.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8oqcC ![]() 8oqdC ![]() 8oqeC ![]() 8oqgC 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 197 molecules ![](data/chem/img/FMT.gif)
![](data/chem/img/F3I.gif)
![](data/chem/img/VVU.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F3I.gif)
![](data/chem/img/VVU.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-F3I / ( | #4: Chemical | ChemComp-VVU / | #5: Chemical | ChemComp-CL / | #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: 3.08 Å3/Da / Density % sol: 60.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 2.5 M NaCl 3.3 M HCOONa 0.1 M Acetate buffer / PH range: 4.7-5.2 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 1, 2022 |
Radiation | Monochromator: Cu filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→22.06 Å / Num. obs: 27241 / % possible obs: 99.3 % / Redundancy: 1.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.056 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 1.8 % / Rmerge(I) obs: 1.296 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1303 / CC1/2: 0.199 / Rsym value: 1.296 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.63 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→22.06 Å
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Refine LS restraints |
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LS refinement shell |
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