PDB-9fyw: X-ray structure of the adduct formed upon reaction of RNase A wit...

ID or keywords:

Entry

Database: PDB / ID: 9fyw

Title

X-ray structure of the adduct formed upon reaction of RNase A with [Ru2Cl(D-p-CNPhF)(O2CCH3)3]

Components

Ribonuclease pancreatic

Keywords

HYDROLASE / Diruthenium / Protein interaction / Metallodrug

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: 1.4 Å

Authors

Teran, A. / Ferraro, G. / Merlino, A.

Funding support

1items

Citation

Journal: Inorg Chem Front / Year: 2024
Title: Exchange of equatorial ligands in protein-bound paddlewheel Ru25+ complexes: new insights from X-ray crystallography and quantum chemistry
Authors: Teran, A. / Fasulo, F. / Ferraro, G. / Sanchez-Pelaez, A.E. / Herrero, S. / Pavone, M. / Munoz-Garcia, A.B. / Merlino, A.

History

Deposition	Jul 4, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 27, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9fyw.cif.gz	76.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9fyw.ent.gz		Display	PDB format
PDBx/mmJSON format	9fyw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fy/9fyw ftp://data.pdbj.org/pub/pdb/validation_reports/fy/9fyw	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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)

Deposited unit

A: Ribonuclease pancreatic

B: Ribonuclease pancreatic

hetero molecules

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

1

A: Ribonuclease pancreatic

hetero molecules

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

2

B: Ribonuclease pancreatic

hetero molecules

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

Unit cell

Length a, b, c (Å)	100.620, 32.740, 72.250
Angle α, β, γ (deg.)	90.000, 90.290, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-322- HOH
2	1	B-313- HOH
3	1	B-435- HOH
4	1	B-461- HOH
5	1	B-466- HOH

#1: Protein	Ribonuclease pancreatic Mass: 16480.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61823
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-A1IHW / 4-[11-(4-cyanophenyl)-1,5-bis($l^{1}-oxidanyl)-3,7-dimethyl-2,4,6,8-tetraoxa-9,11-diaza-1$l^{5},5$l^{5}-diruthenatricyclo[3.3.3.0^{1,5}]undecan-9-yl]benzenecarbonitrile Mass: 602.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₂₀N₄O₆Ru₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.04 Å³/Da / Density % sol: 39.68 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: Free-interface diffusion of a 10 uL of 30 mg/ml protein solution, 20 mM sodium citrate at pH 5.3 agaist 10 ul isopropanol 99.9% isopropanol

-
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: Jul 16, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.4→72.25 Å / Num. obs: 36934 / % possible obs: 91 % / Redundancy: 5.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.048 / Net I/σ(I): 19.4
Reflection shell	Resolution: 1.4→1.53 Å / R_merge(I) obs: 0.494 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 960 / CC_1/2: 0.82

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.4→72.249 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.948 / SU B: 1.344 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2143	1758	4.76 %
R_work	0.1745	35176	-
all	0.176	-	-
obs	-	36934	78.803 %

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: 19.483 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.001 Å²	-0 Å²	-0 Å²
2-	-	-0 Å²	-0 Å²
3-	-	-	-0.001 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→72.249 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1894	0	36	308	2238

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	2062
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1775
X-RAY DIFFRACTION	r_angle_refined_deg	1.756	1.829	2826
X-RAY DIFFRACTION	r_angle_other_deg	0.607	1.774	4123
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.041	5	268
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.073	5	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.478	10	341
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.178	10	92
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	303
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	2486
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	464
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	412
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.2	0.2	1707
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	1011
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1075
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	219
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.159	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.2	0.2	22
X-RAY DIFFRACTION	r_nbd_other	0.185	0.2	90
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.172	0.2	54
X-RAY DIFFRACTION	r_mcbond_it	2.539	2.082	1045
X-RAY DIFFRACTION	r_mcbond_other	2.539	2.082	1045
X-RAY DIFFRACTION	r_mcangle_it	4.041	3.737	1322
X-RAY DIFFRACTION	r_mcangle_other	4.039	3.737	1323
X-RAY DIFFRACTION	r_scbond_it	2.792	2.266	1017
X-RAY DIFFRACTION	r_scbond_other	2.802	2.248	985
X-RAY DIFFRACTION	r_scangle_it	4.393	4.07	1506
X-RAY DIFFRACTION	r_scangle_other	4.445	4.005	1446
X-RAY DIFFRACTION	r_lrange_it	8.439	25.773	2451
X-RAY DIFFRACTION	r_lrange_other	8.383	21.68	2315

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
1.4-1.436	0.303	16	0.316	376	0.315	3444	0.958	0.93	11.3821	0.306
1.436-1.476	0.29	49	0.281	917	0.281	3345	0.961	0.945	28.8789	0.267
1.476-1.519	0.312	77	0.269	1388	0.271	3258	0.939	0.952	44.9662	0.252
1.519-1.565	0.275	82	0.241	1753	0.243	3163	0.95	0.96	58.0145	0.214
1.565-1.617	0.223	101	0.21	2043	0.211	3036	0.967	0.971	70.6192	0.181
1.617-1.673	0.234	120	0.196	2423	0.198	2977	0.967	0.975	85.4216	0.168
1.673-1.736	0.206	146	0.176	2741	0.178	2891	0.974	0.98	99.8616	0.152
1.736-1.807	0.23	100	0.157	2673	0.16	2773	0.97	0.985	100	0.135
1.807-1.888	0.185	144	0.175	2496	0.176	2641	0.977	0.981	99.9621	0.156
1.888-1.98	0.214	132	0.176	2386	0.178	2528	0.97	0.981	99.6044	0.161
1.98-2.087	0.236	122	0.177	2306	0.18	2428	0.966	0.981	100	0.167
2.087-2.213	0.206	93	0.173	2199	0.174	2292	0.972	0.982	100	0.166
2.213-2.366	0.243	86	0.17	2066	0.172	2157	0.965	0.982	99.7682	0.167
2.366-2.555	0.205	104	0.161	1918	0.163	2028	0.975	0.983	99.7041	0.165
2.555-2.799	0.217	95	0.161	1764	0.164	1861	0.97	0.983	99.8925	0.17
2.799-3.128	0.219	83	0.159	1592	0.162	1675	0.967	0.984	100	0.173
3.128-3.611	0.19	65	0.162	1436	0.164	1507	0.975	0.984	99.6019	0.184
3.611-4.42	0.213	69	0.151	1201	0.154	1274	0.975	0.986	99.686	0.181
4.42-6.239	0.187	57	0.177	935	0.177	997	0.98	0.985	99.4985	0.224
6.239-72.249	0.233	17	0.244	564	0.244	591	0.968	0.956	98.308	0.295

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi