7QTB

S1 nuclease from Aspergillus oryzae in complex with cytidine-5'-monophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.131 
  • R-Value Work: 0.109 
  • R-Value Observed: 0.110 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Atomic resolution studies of S1 nuclease complexes reveal details of RNA interaction with the enzyme despite multiple lattice-translocation defects.

Adamkova, K.Koval', T.Ostergaard, L.H.Duskova, J.Maly, M.Svecova, L.Skalova, T.Kolenko, P.Dohnalek, J.

(2022) Acta Crystallogr D Struct Biol 78: 1194-1209

  • DOI: https://doi.org/10.1107/S2059798322008397
  • Primary Citation of Related Structures:  
    7QTA, 7QTB

  • PubMed Abstract: 

    S1 nuclease from Aspergillus oryzae is a single-strand-specific nuclease from the S1/P1 family that is utilized in biochemistry and biotechnology. S1 nuclease is active on both RNA and DNA but with differing catalytic efficiencies. This study clarifies its catalytic properties using a thorough comparison of differences in the binding of RNA and DNA in the active site of S1 nuclease based on X-ray structures, including two newly solved complexes of S1 nuclease with the products of RNA cleavage at atomic resolution. Conclusions derived from this comparison are valid for the whole S1/P1 nuclease family. For proper model building and refinement, multiple lattice-translocation defects present in the measured diffraction data needed to be solved. Two different approaches were tested and compared. Correction of the measured intensities proved to be superior to the use of the dislocation model of asymmetric units with partial occupancy of individual chains. As the crystals suffered from multiple lattice translocations, equations for their correction were derived de novo. The presented approach to the correction of multiple lattice-translocation defects may help to solve similar problems in the field of protein X-ray crystallography.


  • Organizational Affiliation

    Institute of Biotechnology, Czech Academy of Sciences, v.v.i., Průmyslová 595, 252 50 Vestec, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclease S1
A, B
267Aspergillus oryzae RIB40Mutation(s): 0 
Gene Names: nucSAO090001000075
EC: 3.1.30.1
UniProt
Find proteins for P24021 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore P24021 
Go to UniProtKB:  P24021
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24021
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C5P (Subject of Investigation/LOI)
Query on C5P

Download Ideal Coordinates CCD File 
I [auth A],
T [auth B]
CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
Q [auth B],
R [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
BTB
Query on BTB

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
U [auth B],
V [auth B]
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A],
S [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
N [auth B]
O [auth B]
C [auth A],
D [auth A],
E [auth A],
N [auth B],
O [auth B],
P [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
W [auth B],
X [auth B],
Y [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.075α = 107.47
b = 48.459β = 90.076
c = 65.547γ = 105.702
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicEuropean UnionLM2018127
European Regional Development FundEuropean UnionCZ.02.1.01/0.0/0.0/15_003/0000447
Czech Science FoundationEuropean Union20-12109S
European Regional Development FundEuropean UnionCZ.02.1.01/0.0/0.0/18_046/0015974

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description