4GSP | pdb_00004gsp

RIBONUCLEASE T1 COMPLEXED WITH 2',3'-CGPS + 3'-GMP, 7 DAYS

• PDB DOI: https://doi.org/10.2210/pdb4GSP/pdb

• Classification: ENDORIBONUCLEASE
• Organism(s): Aspergillus oryzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-12-02 Released: 1998-08-12 
• Deposition Author(s): Zegers, I., Wyns, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.197 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Hydrolysis of a slow cyclic thiophosphate substrate of RNase T1 analyzed by time-resolved crystallography.

Zegers, I., Loris, R., Dehollander, G., Fattah Haikal, A., Poortmans, F., Steyaert, J., Wyns, L.

(1998) Nat Struct Biol 5: 280-283

• PubMed: 9546218 
• DOI: https://doi.org/10.1038/nsb0498-280
• Primary Citation Related Structures: 
  1GSP, 2GSP, 3GSP, 4GSP, 5GSP, 6GSP, 7GSP


• PubMed Abstract: 
  

  Here we present a time-resolved crystallographic analysis of the hydrolysis of exo (Sp) guanosine 2',3'-cyclophosphorothioate by RNase T1. The use of a slow substrate and fast crystallization methods made it possible to perform the study with conventional data-collection techniques. The results support the idea that the hydrolysis reaction proceeds through a mechanism that is the inverse of the transesterification reaction. In addition, the structures provide an explanation for the differential behavior of RNase T1 towards exo- and endo-cyclic thiophosphates.

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Organizational Affiliation: 
• Laboratorium voor Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Belgium. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.86 kDa 
• Atom Count: 981 
• Modeled Residue Count: 104 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE T1	A	104	Aspergillus oryzae	Mutation(s): 0  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3GP	C [auth A]	GUANOSINE-3'-MONOPHOSPHATE C10 H14 N5 O8 P ZDPUTNZENXVHJC-UUOKFMHZSA-N
SGP	D [auth A]	GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE C10 H12 N5 O6 P S QZEROIIFJLCOOE-FHIGPPGSSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.197 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.24	α = 90
b = 51.1	β = 90
c = 40.45	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-08-12 
Deposition Author(s): Zegers, I., Wyns, L.

Revision History  

• Version 1.0: 1998-08-12
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary