9G48

Staphylococcus aureus MazF in complex with Nanobody 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Nanobody-mediated activation and inhibition of Staphylococcus aureus MazF

Prolic-Kalinsek, M.Zorzini, V.Haesaerts, S.De Bruyn, P.Loris, R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoribonuclease MazF
A, B
133Staphylococcus aureusMutation(s): 0 
Gene Names: mazFSA1873
EC: 3.1
UniProt
Find proteins for Q2FWI8 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FWI8 
Go to UniProtKB:  Q2FWI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FWI8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 6
C, D
138Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
G [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PG0
Query on PG0

Download Ideal Coordinates CCD File 
K [auth D]2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth B],
I [auth D],
J [auth D]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.14α = 90
b = 60.14β = 90
c = 246.24γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Vrije Universiteit BrusselBelgiumSRP13

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Structure summary