PDB-9eo8: X-ray structure of the adduct formed upon reaction of picoplatin ...

ID or keywords:

Entry

Database: PDB / ID: 9eo8

Title

X-ray structure of the adduct formed upon reaction of picoplatin with bovine pancreatic ribonuclease (structure D)

Components

Ribonuclease pancreatic

Keywords

RNA BINDING PROTEIN / picoplatin / lysozyme / protein / interaction

Function / homology

Function and homology information

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

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.76 Å

Authors

Ferraro, G. / Merlino, A.

Funding support

1items

Citation

Journal: Dalton Trans / Year: 2024
Title: Picoplatin binding to proteins: X-ray structures and mass spectrometry data on the adducts with lysozyme and ribonuclease A.
Authors: Ferraro, G. / Lyckova, T. / Massai, L. / Starha, P. / Messori, L. / Merlino, A.

History

Deposition	Mar 14, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 22, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Nov 20, 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	9eo8.cif.gz	72.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9eo8.ent.gz		Display	PDB format
PDBx/mmJSON format	9eo8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9eo8_validation.pdf.gz	7.3 MB	Display	wwPDB validaton report
Full document	9eo8_full_validation.pdf.gz	7.3 MB	Display
Data in XML	9eo8_validation.xml.gz	14.4 KB	Display
Data in CIF	9eo8_validation.cif.gz	20.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eo/9eo8 ftp://data.pdbj.org/pub/pdb/validation_reports/eo/9eo8	HTTPS FTP

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Related structure data

Related structure data	9enzC 9eo2C 9eo5C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#9 - Sep 2000 Lysozyme similarity (1) #105 - Sep 2008 Ribonuclease A similarity (8) #143 - Nov 2011 Toll-like Receptors similarity (8) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

AAA: Ribonuclease pancreatic

BBB: Ribonuclease pancreatic

hetero molecules

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

1

AAA: Ribonuclease pancreatic

hetero molecules

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

2

BBB: Ribonuclease pancreatic

hetero molecules

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

Unit cell

Length a, b, c (Å)	100.920, 32.880, 74.000
Angle α, β, γ (deg.)	90.000, 90.308, 90.000
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 2 molecules AAABBB

#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) Gallus gallus (chicken) / References: UniProt: P61824, pancreatic ribonuclease

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Non-polymers , 5 types, 215 molecules

#2: Chemical	ChemComp-NH3 / AMMONIA Mass: 17.031 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NH₃
#3: Chemical	ChemComp-PT / PLATINUM (II) ION Mass: 195.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-A1H58 / azanyl-chloranyl-(2-methylpyridin-1-ium-1-yl)platinum Mass: 339.680 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₉ClN₂Pt / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.24 Å³/Da / Density % sol: 45.07 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 22% PEG4000, 0.1 M 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: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.76→28.83 Å / Num. obs: 24352 / % possible obs: 98.3 % / Redundancy: 6.2 % / CC_1/2: 0.996 / R_merge(I) obs: 0.097 / Net I/σ(I): 10
Reflection shell	Resolution: 1.76→1.81 Å / Redundancy: 6.2 % / R_merge(I) obs: 0.792 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1413 / CC_1/2: 0.792 / % possible all: 98.3

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.76→28.83 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.934 / SU B: 3.123 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.136 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2346	1173	4.817 %
R_work	0.1976	23179	-
all	0.199	-	-
obs	-	24352	99.311 %

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: 28.539 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.07 Å²	-0 Å²	0.143 Å²
2-	-	-0.048 Å²	-0 Å²
3-	-	-	0.117 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→28.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1824	0	40	193	2057

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	1980
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	1663
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.092	0.01	31
X-RAY DIFFRACTION	r_angle_refined_deg	1.605	1.642	2716
X-RAY DIFFRACTION	r_angle_other_deg	1.405	1.581	3911
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.07	5	252
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.38	24.02	102
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.286	15	336
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.004	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	264
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	2300
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	384
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	407
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	1511
X-RAY DIFFRACTION	r_nbtor_refined	0.157	0.2	905
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	785
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.217	0.2	132
X-RAY DIFFRACTION	r_metal_ion_refined	0.593	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.33	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.268	0.2	61
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.463	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	2.428	2.806	990
X-RAY DIFFRACTION	r_mcbond_other	2.428	2.805	989
X-RAY DIFFRACTION	r_mcangle_it	3.639	4.173	1252
X-RAY DIFFRACTION	r_mcangle_other	3.629	4.177	1249
X-RAY DIFFRACTION	r_scbond_it	3.557	3.237	987
X-RAY DIFFRACTION	r_scbond_other	3.556	3.235	988
X-RAY DIFFRACTION	r_scangle_it	5.487	4.692	1493
X-RAY DIFFRACTION	r_scangle_other	5.481	4.689	1492
X-RAY DIFFRACTION	r_lrange_it	7.08	34.551	2173
X-RAY DIFFRACTION	r_lrange_other	7.023	34.186	2116

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.76-1.806	0.289	96	0.272	1600	X-RAY DIFFRACTION	96.2543
1.806-1.855	0.286	66	0.262	1688	X-RAY DIFFRACTION	99.6025
1.855-1.909	0.266	103	0.243	1582	X-RAY DIFFRACTION	100
1.909-1.968	0.233	76	0.218	1595	X-RAY DIFFRACTION	99.7612
1.968-2.032	0.252	82	0.221	1503	X-RAY DIFFRACTION	99.6855
2.032-2.103	0.248	72	0.21	1476	X-RAY DIFFRACTION	99.9354
2.103-2.183	0.254	62	0.193	1450	X-RAY DIFFRACTION	99.8679
2.183-2.272	0.288	75	0.19	1367	X-RAY DIFFRACTION	99.9307
2.272-2.373	0.21	56	0.201	1302	X-RAY DIFFRACTION	97.8386
2.373-2.488	0.241	63	0.196	1257	X-RAY DIFFRACTION	99.8487
2.488-2.623	0.23	53	0.201	1216	X-RAY DIFFRACTION	99.8426
2.623-2.782	0.263	71	0.198	1119	X-RAY DIFFRACTION	99.665
2.782-2.973	0.254	55	0.192	1085	X-RAY DIFFRACTION	99.9124
2.973-3.211	0.241	61	0.19	988	X-RAY DIFFRACTION	99.4313
3.211-3.517	0.218	40	0.178	935	X-RAY DIFFRACTION	99.4898
3.517-3.931	0.217	51	0.173	821	X-RAY DIFFRACTION	98.7542
3.931-4.537	0.18	34	0.149	739	X-RAY DIFFRACTION	99.7419
4.537-5.551	0.168	25	0.158	648	X-RAY DIFFRACTION	99.5562
5.551-7.829	0.236	28	0.227	501	X-RAY DIFFRACTION	98.8785
7.829-28.83	0.364	4	0.297	301	X-RAY DIFFRACTION	96.519

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