9FYW | pdb_00009fyw

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

PDB DOI: https://doi.org/10.2210/pdb9FYW/pdb

Classification: HYDROLASE
Organism(s): Bos taurus
Mutation(s): No

Deposited: 2024-07-04 Released: 2024-11-27
Deposition Author(s): Teran, A., Ferraro, G., Merlino, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.214 (Depositor), 0.228 (DCC)
R-Value Work:
0.174 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Exchange of equatorial ligands in protein-bound paddlewheel Ru25+ complexes: new insights from X-ray crystallography and quantum chemistry

Teran, A., Fasulo, F., Ferraro, G., Sanchez-Pelaez, A.E., Herrero, S., Pavone, M., Munoz-Garcia, A.B., Merlino, A.

(2024) Inorg Chem Front 11: 7803-7811

DOI: https://doi.org/10.1039/D4QI01846J

Macromolecule Content

Total Structure Weight: 33.66 kDa
Atom Count: 2,327
Modeled Residue Count: 248
Deposited Residue Count: 300
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A, B	150	Bos taurus	Mutation(s): 0 EC: 4.6.1.18
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823 Go to UniProtKB: P61823
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61823
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IHW (Subject of Investigation/LOI) Query on A1IHW Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	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 C₁₉ H₂₀ N₄ O₆ Ru₂ RVPMMJARIZYFTQ-UHFFFAOYSA-L		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.214 (Depositor), 0.228 (DCC)
R-Value Work: 0.174 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.62	α = 90
b = 32.74	β = 90.29
c = 72.25	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-11-27
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.