[English] 日本語
Yorodumi- PDB-8oqf: Cross-linked crystal of Dirhodium tetraacetate/ribonuclease A add... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8oqf | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cross-linked crystal of Dirhodium tetraacetate/ribonuclease A adduct in the P3221 space group (low 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: 1.5 Å | |||||||||||||||
Authors | Loreto, D. / Merlino, A. / Maity, B. / Ueno, T. | |||||||||||||||
Funding support | Italy, Japan, 4items
| |||||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8oqf.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8oqf.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 8oqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oqf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8oqf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8oqf_validation.xml.gz | 10 KB | Display | |
Data in CIF | 8oqf_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/8oqf ftp://data.pdbj.org/pub/pdb/validation_reports/oq/8oqf | HTTPS FTP |
-Related structure data
Related structure data | 8oqcC 8oqdC 8oqeC 8oqgC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|
-Non-polymers , 5 types, 197 molecules
#2: Chemical | #3: Chemical | ChemComp-F3I / ( | #4: Chemical | ChemComp-VVU / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.07 % |
---|---|
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 |
---|---|
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 | 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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→22.06 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.088 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.078 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→22.06 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|