1I0X

RIBONUCLEASE T1 IN COMPLEX WITH 2'GMP (FORM II CRYSTAL)

PDB DOI: https://doi.org/10.2210/pdb1I0X/pdb

Classification: HYDROLASE
Organism(s): Aspergillus oryzae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2001-01-30 Released: 2001-02-14
Deposition Author(s): De Swarte, J., De Vos, S., Langhorst, U., Steyaert, J., Loris, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.216
R-Value Work: 0.190
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The contribution of metal ions to the conformational stability of ribonuclease T1: crystal versus solution.

Deswarte, J., De Vos, S., Langhorst, U., Steyaert, J., Loris, R.

(2001) Eur J Biochem 268: 3993-4000

PubMed: 11453993 Search on PubMed
DOI: https://doi.org/10.1046/j.1432-1327.2001.02310.x
Primary Citation of Related Structures:
1HYF, 1HZ1, 1I0V, 1I0X

PubMed Abstract:
In the crystalline state, ribonuclease T1 binds calcium ions at different lattice-dependent positions. In solution, its conformational stability is also remarkably increased in the presence of divalent metal ions. Combining urea unfolding studies and X-ray crystallography, we compared the presence of several metal ions at specific sites in the protein to their contribution to the overall stabilizing effect in solution. We constructed thermodynamic cycles involving particular metal ions and specific carboxylate functions. The resulting coupling energies indicate that some (but not all) metal ions found at lattice contacts in crystal structures may indeed significantly contribute to stability enhancement in the presence of metal ions in solution.

Organizational Affiliation

Laboratorium voor Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Belgium.

Macromolecule Content

Total Structure Weight: 46.4 kDa
Atom Count: 3,750
Modelled Residue Count: 415
Deposited Residue Count: 416
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GUANYL-SPECIFIC RIBONUCLEASE T1	A, B, C, D	104	Aspergillus oryzae	Mutation(s): 1 EC: 3.1.27.3 (PDB Primary Data), 4.6.1.24 (UniProt)
UniProt
Find proteins for P00651 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore P00651 Go to UniProtKB: P00651
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00651
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2GP Query on 2GP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth D] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C]	E [auth A], H [auth B], J [auth C], K [auth C], N [auth D]	GUANOSINE-2'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P WTIFIAZWCCBCGE-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain L [auth D] SDF format, chain M [auth D] SDF format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] MOL2 format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D] mmCIF format, chain F [auth B]	F [auth B], G [auth B], I [auth C], L [auth D], M [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D] Focus chain M [auth D]