PDB-7pni: X-ray structure of the adduct formed upon reaction of Pt(II) comp...

ID or keywords:

Entry

Database: PDB / ID: 7pni

Title

X-ray structure of the adduct formed upon reaction of Pt(II) complex 2c with ribonuclease A

Components

Ribonuclease pancreatic

Keywords

RNA BINDING PROTEIN / metallodrug / platinum / protein interaction / Pt-protein adduct

Function / homology

Function and homology information

pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function

Biological species

Bos taurus (domestic cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.13 Å

Authors

Ferraro, G. / Merlino, A.

Funding support

1items

Citation

Journal: Int J Mol Sci / Year: 2021
Title: Reactions with Proteins of Three Novel Anticancer Platinum(II) Complexes Bearing N-Heterocyclic Ligands.
Authors: Sacco, F. / Tarchi, M. / Ferraro, G. / Merlino, A. / Facchetti, G. / Rimoldi, I. / Messori, L. / Massai, L.

History

Deposition	Sep 7, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7pni.cif.gz	68.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7pni.ent.gz		Display	PDB format
PDBx/mmJSON format	7pni.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pn/7pni ftp://data.pdbj.org/pub/pdb/validation_reports/pn/7pni	HTTPS FTP

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Related structure data

Related structure data	7pnhC 1jvtS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3lxo-d 5e5e-2 6qmn-1 1jvu-1 3eux-1 3rat-d 3d8z-1 3d6o-1 3d6p-1 3jw1-2 5jml-1 1wbu-1 1a5q-d 1rhb-d 1w4p-1 6qmn-3 5rat-d 1c9x-d 6xhe-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

7pnhC

1jvtS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#105 - Sep 2008 Ribonuclease A similarity (9) #143 - Nov 2011 Toll-like Receptors similarity (9) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

AAA: Ribonuclease pancreatic

BBB: Ribonuclease pancreatic

hetero molecules

28.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Ribonuclease pancreatic

hetero molecules

defined by author
14.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: Ribonuclease pancreatic

hetero molecules

defined by author
14.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	100.140, 31.790, 73.740
Angle α, β, γ (deg.)	90.000, 90.347, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Ribonuclease pancreatic / RNase 1 / RNase A Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical	ChemComp-PT / PLATINUM (II) ION Mass: 195.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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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: 42.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG4K 10 mM sodium citrate pH 5.1

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.96 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96 Å / Relative weight: 1
Reflection	Resolution: 2.13→28.04 Å / Num. obs: 13153 / % possible obs: 99 % / Redundancy: 6.2 % / CC_1/2: 0.998 / R_merge(I) obs: 0.078 / R_pim(I) all: 0.034 / R_rim(I) all: 0.086 / Net I/σ(I): 14.5
Reflection shell	Resolution: 2.13→2.17 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.643 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 649 / CC_1/2: 0.898 / R_pim(I) all: 0.318 / R_rim(I) all: 0.721 / % possible all: 97.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
MOSFLM		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1jvt

1jvt

Resolution: 2.13→28.04 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.903 / SU B: 7.018 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / ESU R: 0.296 / ESU R Free: 0.245
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.275	674	5.134 %
R_work	0.1923	12454	-
all	0.197	-	-
obs	-	13128	98.183 %

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

B_iso mean: 39.806 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.143 Å²	0 Å²	-0.192 Å²
2-	-	-0.072 Å²	0 Å²
3-	-	-	0.217 Å²

Refinement step

Cycle: LAST / Resolution: 2.13→28.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1885	0	5	139	2029

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1968
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	1675
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.004	0.01	9
X-RAY DIFFRACTION	r_angle_refined_deg	2.195	1.675	2679
X-RAY DIFFRACTION	r_angle_other_deg	1.322	1.578	3937
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.775	5	254
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.316	23.918	97
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.553	15	333
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.093	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	272
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2267
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	382
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	395
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	1575
X-RAY DIFFRACTION	r_nbtor_refined	0.16	0.2	930
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	877
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.204	0.2	105
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.136	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.198	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.223	0.2	72
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.168	0.2	19
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.028	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	3.912	4.161	1010
X-RAY DIFFRACTION	r_mcbond_other	3.913	4.159	1009
X-RAY DIFFRACTION	r_mcangle_it	6.109	6.202	1268
X-RAY DIFFRACTION	r_mcangle_other	6.105	6.205	1267
X-RAY DIFFRACTION	r_scbond_it	4.178	4.453	954
X-RAY DIFFRACTION	r_scbond_other	4.174	4.453	954
X-RAY DIFFRACTION	r_scangle_it	6.656	6.534	1420
X-RAY DIFFRACTION	r_scangle_other	6.465	6.53	1414
X-RAY DIFFRACTION	r_lrange_it	9.283	49.226	2140
X-RAY DIFFRACTION	r_lrange_other	9.28	49.187	2129

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.13-2.185	0.429	34	0.286	816	0.292	963	0.764	0.78	88.2658	0.242
2.185-2.244	0.307	41	0.257	880	0.259	949	0.815	0.833	97.0495	0.225
2.244-2.309	0.346	38	0.244	866	0.248	924	0.827	0.879	97.8355	0.207
2.309-2.38	0.369	47	0.225	852	0.232	901	0.839	0.895	99.778	0.186
2.38-2.457	0.367	40	0.202	815	0.209	868	0.827	0.897	98.5023	0.171
2.457-2.543	0.341	41	0.208	780	0.214	822	0.864	0.908	99.8783	0.175
2.543-2.638	0.303	45	0.182	785	0.188	832	0.89	0.927	99.7596	0.164
2.638-2.745	0.291	42	0.181	728	0.186	774	0.891	0.931	99.4832	0.166
2.745-2.865	0.279	50	0.189	700	0.196	751	0.902	0.924	99.8668	0.18
2.865-3.004	0.284	51	0.191	652	0.198	709	0.885	0.924	99.1537	0.184
3.004-3.164	0.267	40	0.193	656	0.197	697	0.903	0.932	99.8565	0.19
3.164-3.353	0.245	30	0.178	627	0.181	662	0.937	0.949	99.2447	0.184
3.353-3.581	0.203	20	0.165	583	0.166	608	0.926	0.957	99.1776	0.177
3.581-3.863	0.301	33	0.175	539	0.182	576	0.902	0.94	99.3056	0.197
3.863-4.224	0.209	17	0.161	507	0.163	525	0.944	0.944	99.8095	0.19
4.224-4.709	0.168	34	0.153	455	0.154	489	0.967	0.963	100	0.186
4.709-5.412	0.274	27	0.159	413	0.165	444	0.915	0.962	99.0991	0.197
5.412-6.567	0.142	9	0.224	356	0.222	369	0.894	0.925	98.916	0.278
6.567-9.043	0.28	22	0.245	264	0.248	294	0.899	0.903	97.2789	0.303
9.043-28.042	0.446	12	0.257	172	0.268	197	0.88	0.918	93.401	0.31

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