6XVX | pdb_00006xvx

X-ray structure obtained upon reaction of dirhodium tetraacetate with RNase A (high resolution)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.233 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.196 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6XVX

This is version 1.3 of the entry. See complete history. 

Literature

Protein interactions of dirhodium tetraacetate: a structural study.

Ferraro, G., Pratesi, A., Messori, L., Merlino, A.

(2020) Dalton Trans 49: 2412-2416

  • DOI: https://doi.org/10.1039/c9dt04819g
  • Primary Citation Related Structures: 
    6XVX, 6XW0

  • PubMed Abstract: 

    The interactions between the cytotoxic paddlewheel dirhodium complex [Rh2(μ-O2CCH3)4] and the model protein bovine pancreatic ribonuclease (RNase A) were investigated by high-resolution mass spectrometry and X-ray crystallography. The results indicate that [Rh2(μ-O2CCH3)4] extensively reacts with RNase A. The metal compound binds the protein via coordination of the imidazole ring of a His side chain to one of its axial sites, while the dirhodium center and the acetato ligands remain unmodified. Data provide valuable information for the design of artificial dirhodium-containing metalloenzymes.

    • Organizational Affiliation: 
    • Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia, 3-13, 50019, Sesto Fiorentino, Florence, Italy. luigi.messori@unifi.it.

Macromolecule Content 

  • Total Structure Weight: 29.24 kDa 
  • Atom Count: 2,385 
  • Modeled Residue Count: 248 
  • Deposited Residue Count: 248 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribonuclease pancreaticA [auth AAA],
B [auth BBB]		124Bos taurusMutation(s): 0 
EC: 4.6.1.18
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61823
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RH3
(Subject of Investigation/LOI)

Query on RH3


Download:Ideal Coordinates CCD File
AA [auth BBB]
K [auth AAA]
L [auth AAA]
M [auth AAA]
N [auth AAA]
AA [auth BBB],
K [auth AAA],
L [auth AAA],
M [auth AAA],
N [auth AAA],
X [auth BBB],
Y [auth BBB],
Z [auth BBB]
RHODIUM(III) ION
Rh
PZSJYEAHAINDJI-UHFFFAOYSA-N
ACT

Query on ACT


Download:Ideal Coordinates CCD File
C [auth AAA]
D [auth AAA]
E [auth AAA]
F [auth AAA]
G [auth AAA]
C [auth AAA],
D [auth AAA],
E [auth AAA],
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth AAA],
J [auth AAA],
O [auth BBB],
P [auth BBB],
Q [auth BBB],
R [auth BBB],
S [auth BBB],
T [auth BBB],
U [auth BBB],
V [auth BBB],
W [auth BBB]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.233 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.196 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.43α = 90
b = 32.75β = 90.38
c = 72.69γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItaly22578

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary