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Yorodumi- PDB-5jml: X-ray structure of the complex between bovine pancreatic ribonucl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jml | ||||||
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Title | X-ray structure of the complex between bovine pancreatic ribonuclease and penthachlorocarbonyliridate(III) (2 months of soaking) | ||||||
Components | Ribonuclease pancreaticPancreatic ribonuclease family | ||||||
Keywords | HYDROLASE / iridium compound / CORM / protein iridium interaction | ||||||
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: 2.29 Å | ||||||
Authors | Caterino, M. / Petruk, A.A. / Vergara, A. / Ferraro, G. / Merlino, A. | ||||||
Citation | Journal: Dalton Trans / Year: 2016 Title: Mapping the protein-binding sites for iridium(iii)-based CO-releasing molecules. Authors: Caterino, M. / Petruk, A.A. / Vergara, A. / Ferraro, G. / Marasco, D. / Doctorovich, F. / Estrin, D.A. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jml.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jml.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 5jml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/5jml ftp://data.pdbj.org/pub/pdb/validation_reports/jm/5jml | HTTPS FTP |
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-Related structure data
Related structure data | 5jmgC 1jvtS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 1 - 124 / Label seq-ID: 1 - 124
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5 |
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-Non-polymers , 5 types, 84 molecules
#2: Chemical | ChemComp-IR / #3: Chemical | ChemComp-O / | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-CMO / #6: Water | ChemComp-HOH / | |
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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: 2.14 Å3/Da / Density % sol: 42.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG4K, 10 mM soium citrate pH 5.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→72.59 Å / Num. obs: 10756 / % possible obs: 96.5 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 1.72 |
Reflection shell | Resolution: 2.29→2.34 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JVT Resolution: 2.29→72.59 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.89 / SU B: 11.091 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.576 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.745 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→72.59 Å
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Refine LS restraints |
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