Index of /cvmfsmonitor/repository/facilities.gridpp.ac.uk/ccp4/release-7.0-updated/ccp4-7.0/share/ccp4i2/demo_data/rnase

	Name	Last modified	Size	Description
	Parent Directory		-
	1mgw.pdb	2018-04-05 16:35	178K
	1sar.pdb	2018-04-05 16:35	174K
	2GMP_smiles.txt	2018-04-05 16:35	65
	3GMP_smiles.txt	2018-04-05 16:35	65
	3a5e.pdb	2018-04-05 16:35	94K
	INFO.txt	2018-04-05 16:35	182
	rnase.fasta	2018-04-05 16:35	108
	rnase18_Nat_Complexe..>	2018-04-05 16:35	709K
	rnase25_Nat_Derivs.mtz	2018-04-05 16:35	518K
	rnase_model.pdb	2018-04-05 16:35	136K

CCP4i2 demo data: RNAse (PDB:1SAR)

This structure can be solved (1) by experimental phasing using SAD or SIRAS, or (2) by molecular replacement. In addition, there are data for two complexes allowing automated or manual ligand fitting.

Reference for the structure of ribonuclease from Streptomyces aureofaciens (RNase Sa) and its complex with guanosine 3′monophosphate, 3′GMP: Sevcik, J., Dodson, E. J., & Dodson, G. G. (1991). Determination and restrained least-squares refinement of the structures of ribonuclease Sa and its complex with 3′guanylic acid at 1.8 Å resolution. Acta Crystallographica Section B: Structural Science, 47(2), 240-253.

Experimental phasing

The structure was first solved using heavy atom derivatives. Data for three derivatives (Hg, I and Pt), including the anomalous components (collected using CuKα radiation) can be loaded from the first mtz file (rnase25_Nat_Derivs.mtz), which also contains the native enzyme data, all at 2.5 Å resolution. This MTZ file contains structure factor amplitudes (not intensities) for both data sets.

The native data are in the columns labelled:

Column FNAT SIGFNAT

And the derivative data are in the columns labelled:

Column FHG(+) SIGFHG(+) FHG(-) SIGFHG(-)

Column FI(+) SIGFI(+) FI(-) SIGFI(-)

Column FPTNCD25(+) SIGFPTNCD25(+) FPTNCD25(-) SIGFPTNCD25(-)

The structure can be solved using the CRANK2 or SHELXCDE pipelines, using SAD or SIRAS. The Pt is the best derivative, and there are estimated to be around 5 Pt atoms per monomer. The Hg derivative does now lead to a simple solution – the structures was originally solved by MIR.

Molecular Replacement

PDB files for two models are provided. Both lead to a straightforward solution allowing rebuilding with Buccaneer. Other models can be found using the MrBUMP-CCP4mg Task, starting from the sequence.

Ligand Fitting

Amplitudes for the ligand complexes and a higher resolution native set are in the 1.8 Å data file. These can be used for manual or automated Ligand Fitting. The names, PDB codes for the complexes, 3 letter ligand code and canonical smiles strings for the ligands are:

3′GMP PDB: 2SAR 3GP

c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)OP(=O)(O)O)O)N=C(NC2=O)N

2′GMP PDB: 3DGY 2GP

c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)OP(=O)(O)O)N=C(NC2=O)N

Data files

• rnase.fasta - RNAse sequence
• rnase18_Nat_Complexes.mtz - MTZ file containing native amplitudes to 1.8 Å plus two complexes, the first with 3′GMP (3GP) and the second with 2′GMP (2GP).
• rnase25_Nat_Derivs.mtz - MTZ file containing native amplitudes to 2.5 Å plus three heavy atom derivatives with anomalous data, Hg, PT and I.
• rnase_model.pdb Refined structure.
• 1sar.pdb - Refined apo-native 1.8 Å structure.
• 3a5e.pdb - MR model with 95% sequence identify.
• 1mgw.pdb - MR model with 69% sequence identify.
• 3GMP_smiles.txt - smiles string for 3′GMP
• 2GMP_smiles.txt - smiles string for 2′GMP