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Yorodumi- PDB-8oqg: Cross-linked crystal of dirhodium tetraacetate/ribonuclease A add... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oqg | |||||||||||||||
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Title | Cross-linked crystal of dirhodium tetraacetate/ribonuclease A adduct in the P3221 space group (high temperature data collection) | |||||||||||||||
Components | Ribonuclease pancreatic | |||||||||||||||
Keywords | HYDROLASE / Metal/protein adduct / dirhodium tetraacettate / catalysis / porous material | |||||||||||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) | |||||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||||||||
Authors | Loreto, D. / Merlino, A. / Maity, B. / Ueno, T. | |||||||||||||||
Funding support | Italy, Japan, 4items
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Citation | Journal: Inorg.Chem. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oqg.cif.gz | 43.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oqg.ent.gz | 30.3 KB | Display | PDB format |
PDBx/mmJSON format | 8oqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/8oqg ftp://data.pdbj.org/pub/pdb/validation_reports/oq/8oqg | HTTPS FTP |
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-Related structure data
Related structure data | 8oqcC 8oqdC 8oqeC 8oqfC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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) Bos taurus (cattle) / References: UniProt: P61823, pancreatic ribonuclease |
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-Non-polymers , 5 types, 131 molecules
#2: Chemical | ChemComp-VVU / |
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#3: Chemical | ChemComp-VW5 / |
#4: Chemical | ChemComp-FMT / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
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: 3.14 Å3/Da / Density % sol: 60.84 % |
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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: 273 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5406 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jul 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→22.02 Å / Num. obs: 23142 / % possible obs: 99.9 % / Redundancy: 1.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.079 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 1.8 % / Rmerge(I) obs: 1.062 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1111 / CC1/2: 0.339 / Rpim(I) all: 1.062 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→22.02 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.433 / SU ML: 0.074 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.077 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: 21.27 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→22.02 Å
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Refine LS restraints |
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LS refinement shell |
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