5FB9

S1 nuclease from Aspergillus oryzae with unoccupied active site

  • Classification: HYDROLASE
  • Organism(s): Aspergillus oryzae RIB40
  • Expression System: Aspergillus oryzae
  • Mutation(s): No 

  • Deposited: 2015-12-14 Released: 2016-12-28 
  • Deposition Author(s): Koval, T., Oestergaard, L.H., Dohnalek, J.
  • Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic, BIOCEV: Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University from the European Regional Development Fund, European Community

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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



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: nucS, AO090001000075
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
N [auth B],
O [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 
H [auth A],
J [auth B]		2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
K [auth B]
L [auth B]
C [auth A],
D [auth A],
E [auth A],
K [auth B],
L [auth B],
M [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
I [auth A],
P [auth B]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.184α = 107.37
b = 48.595β = 90.13
c = 65.469γ = 105.72
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLG14009
BIOCEV: Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University from the European Regional Development FundCzech RepublicCZ.1.05/1.1.00/02.0109
European Community283570/8787

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Author supporting evidence, Data collection, Derived calculations, Structure summary