- PDB-5e5f: X-ray structure of the complex between RNase A and compound 4-PF6... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5e5f
Title
X-ray structure of the complex between RNase A and compound 4-PF6 ([(PPh3)Au(mi-pbi)Pt(Me)(DMSO)][PF6]), the heterobimetallic derivative obtained in the reaction between the organometallic compound [Pt(pbi)(Me)(DMSO)], pbi=2-(2'-pyridil)benzimidazole (compound 3) and the gold(I) compound [Au(Ph3P)][PF6]
Components
Ribonuclease pancreatic
Keywords
HYDROLASE
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
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 1.95 Å3/Da / Density % sol: 37.06 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop Details: RNase A crystals were obtained using the procedure previously described by Vitagliano et al., 200028. Briefly, crystals of the protein were grown by hanging drop vapor diffusion method using ...Details: RNase A crystals were obtained using the procedure previously described by Vitagliano et al., 200028. Briefly, crystals of the protein were grown by hanging drop vapor diffusion method using a reservoir solution containing 22-24 % (w/v) PEG4K, 10 mM sodium citrate pH 5.1-5.3. The crystals are monoclinic, space group C2, with two molecules in the asymmetric unit. The adducts were prepared by a three-days soaking in a solution that comprised the standard mother liquor used for the crystal growth to which a 2.5-5 mM solution of each compound was added. Crystal soaked in this solution were mounted for the X-ray data collection without using a cryoprotectant, as done in previous studies30. PH range: 5.1-5.3
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 1.68→69 Å / Num. obs: 23228 / % possible obs: 95 % / Redundancy: 2.4 % / Net I/σ(I): 6.5
Reflection shell
Resolution: 1.68→1.71 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 2 / % possible all: 88.5
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0049
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHASER
phasing
Refinement
Resolution: 1.68→69 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.153 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23404
1188
5.1 %
RANDOM
Rwork
0.18332
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obs
0.18601
22040
94.71 %
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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