PDB-7npm: X-ray structure of the adduct formed upon reaction of oxaliplatin...

ID or keywords:

Entry

Database: PDB / ID: 7npm

Title

X-ray structure of the adduct formed upon reaction of oxaliplatin with human angiogenin

Components

Angiogenin

Keywords

HYDROLASE / Oxaliplatin / Cancer / Angiogenesis / Protein metallation / Angiogenin

Function / homology

Function and homology information

activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation / homeostatic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.86 Å

Authors

Ferraro, G. / Merlino, A.

Funding support

Italy, 1items

Citation

Journal: J.Inorg.Biochem. / Year: 2022
Title: Oxaliplatin inhibits angiogenin proliferative and cell migration effects in prostate cancer cells.
Authors: Marzo, T. / Ferraro, G. / Cucci, L.M. / Pratesi, A. / Hansson, O. / Satriano, C. / Merlino, A. / La Mendola, D.

History

Deposition	Feb 27, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 23, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 12, 2023	Group: Database references / Derived calculations / Category: atom_type / citation Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7npm.cif.gz	44.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7npm.ent.gz		Display	PDB format
PDBx/mmJSON format	7npm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7npm_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	7npm_full_validation.pdf.gz	1.7 MB	Display
Data in XML	7npm_validation.xml.gz	8.3 KB	Display
Data in CIF	7npm_validation.cif.gz	10.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/np/7npm ftp://data.pdbj.org/pub/pdb/validation_reports/np/7npm	HTTPS FTP

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Related structure data

Related structure data	5eopS S: Starting model for refinement
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	#234 - Jun 2019 MDM2 and Cancer similarity (1) #105 - Sep 2008 Ribonuclease A similarity (7) #143 - Nov 2011 Toll-like Receptors similarity (7) #255 - Mar 2021 Cisplatin and DNA similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (1)

Deposited unit

AAA: Angiogenin

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	37.720, 85.890, 33.390
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	AAA-311- HOH
2	1	AAA-373- HOH

#1: Protein	Angiogenin / Ribonuclease 5 / RNase 5 Mass: 13943.792 Da / Num. of mol.: 1 / Fragment: UNP residues 26-166 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANG, RNASE5 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical	ChemComp-PT / PLATINUM (II) ION Mass: 195.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pt / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-TAR / D(-)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₆
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 1.94 Å³/Da / Density % sol: 36.58 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 10 % PEG6K, 20 mM sodium citrate pH 5.1, 0.2 M sodium/potassium tartrate

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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: Nov 19, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96 Å / Relative weight: 1
Reflection	Resolution: 1.86→42.945 Å / Num. obs: 9691 / % possible obs: 99.9 % / Redundancy: 11.8 % / CC_1/2: 0.995 / R_merge(I) obs: 0.171 / R_pim(I) all: 0.052 / Net I/σ(I): 10.5
Reflection shell	Resolution: 1.86→1.89 Å / Redundancy: 10.7 % / R_merge(I) obs: 1.22 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 475 / CC_1/2: 0.803 / R_pim(I) all: 0.387 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5EOP

5eop

Resolution: 1.86→42.94 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.912 / SU B: 4.18 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.176 / ESU R Free: 0.174
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2537	463	4.965 %
R_work	0.1782	8862	-
all	0.182	-	-
obs	-	9325	96.923 %

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: 25.6 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.037 Å²	-0 Å²	-0 Å²
2-	-	-0.334 Å²	0 Å²
3-	-	-	0.297 Å²

Refinement step

Cycle: LAST / Resolution: 1.86→42.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	976	0	13	83	1072

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1090
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	966
X-RAY DIFFRACTION	r_angle_refined_deg	1.628	1.674	1484
X-RAY DIFFRACTION	r_angle_other_deg	1.372	1.59	2254
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.54	5	137
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	23.772	19.718	71
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.12	15	187
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.451	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	140
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1268
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	258
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	196
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	873
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	486
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	472
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.197	0.2	62
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.07	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.231	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.206	0.2	53
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.226	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	2.415	2.381	521
X-RAY DIFFRACTION	r_mcbond_other	2.413	2.373	520
X-RAY DIFFRACTION	r_mcangle_it	3.932	3.566	661
X-RAY DIFFRACTION	r_mcangle_other	3.929	3.576	662
X-RAY DIFFRACTION	r_scbond_it	3.283	2.891	569
X-RAY DIFFRACTION	r_scbond_other	3.255	2.883	566
X-RAY DIFFRACTION	r_scangle_it	5.264	4.133	821
X-RAY DIFFRACTION	r_scangle_other	5.261	4.131	820
X-RAY DIFFRACTION	r_lrange_it	8.444	28.493	1173
X-RAY DIFFRACTION	r_lrange_other	8.443	28.521	1174

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 (%)
1.86-1.908	0.286	20	0.259	541	X-RAY DIFFRACTION	82.3789
1.908-1.96	0.333	26	0.239	563	X-RAY DIFFRACTION	85.3623
1.96-2.017	0.306	32	0.222	587	X-RAY DIFFRACTION	94.073
2.017-2.079	0.246	35	0.206	575	X-RAY DIFFRACTION	96.3665
2.079-2.147	0.304	30	0.193	575	X-RAY DIFFRACTION	98.8562
2.147-2.222	0.231	22	0.196	593	X-RAY DIFFRACTION	100
2.222-2.306	0.247	24	0.191	550	X-RAY DIFFRACTION	100
2.306-2.4	0.229	27	0.17	554	X-RAY DIFFRACTION	100
2.4-2.506	0.255	32	0.154	494	X-RAY DIFFRACTION	100
2.506-2.628	0.295	22	0.166	500	X-RAY DIFFRACTION	100
2.628-2.77	0.284	29	0.179	470	X-RAY DIFFRACTION	100
2.77-2.937	0.334	27	0.188	439	X-RAY DIFFRACTION	100
2.937-3.138	0.207	19	0.173	428	X-RAY DIFFRACTION	99.7768
3.138-3.388	0.228	27	0.177	392	X-RAY DIFFRACTION	100
3.388-3.71	0.24	21	0.154	365	X-RAY DIFFRACTION	100
3.71-4.144	0.239	23	0.15	331	X-RAY DIFFRACTION	99.7183
4.144-4.777	0.135	17	0.128	303	X-RAY DIFFRACTION	100
4.777-5.833	0.283	12	0.169	255	X-RAY DIFFRACTION	100
5.833-8.174	0.382	10	0.21	215	X-RAY DIFFRACTION	100

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