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Yorodumi- PDB-8oqd: Dirhodium tetraacetate/ribonuclease A adduct in the P3221 space g... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oqd | |||||||||||||||
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Title | Dirhodium tetraacetate/ribonuclease A adduct in the P3221 space group (1 h soaking) | |||||||||||||||
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: 1.54 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 | 8oqd.cif.gz | 44 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oqd.ent.gz | 31 KB | Display | PDB format |
PDBx/mmJSON format | 8oqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oqd_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8oqd_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8oqd_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 8oqd_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/8oqd ftp://data.pdbj.org/pub/pdb/validation_reports/oq/8oqd | HTTPS FTP |
-Related structure data
Related structure data | 8oqcC 8oqeC 8oqfC 8oqgC 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, 155 molecules
#2: Chemical | ChemComp-D1O / | ||||
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#3: Chemical | ChemComp-FMT / | ||||
#4: Chemical | #5: Chemical | ChemComp-VVU / | #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: 3.08 Å3/Da / Density % sol: 60 % |
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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: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5406 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 24, 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: 1.54→21.98 Å / Num. obs: 25583 / % possible obs: 100 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.041 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.54→1.56 Å / Redundancy: 2.6 % / Rmerge(I) obs: 2.388 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1242 / CC1/2: 0.087 / Rpim(I) all: 1.763 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→21.637 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.363 / SU ML: 0.075 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.079 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: 22.596 Å2
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Refinement step | Cycle: LAST / Resolution: 1.54→21.637 Å
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Refine LS restraints |
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LS refinement shell |
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