6CK7

Crystal structure of a peptide deformylase from Legionella pneumophila bound to actinonin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of a peptide deformylase from Legionella pneumophila bound to actinonin

Edwards, T.E.Horanyi, P.S.Lorimer, D.D.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide deformylase
A, B, C, D
178Legionella pneumophilaMutation(s): 0 
Gene Names: def_2defdef_1def_3A1D14_13265A9P85_13750ERS240541_01674ERS240560_02189ERS253249_00325lpymg_02824
EC: 3.5.1.88
UniProt
Find proteins for Q5ZSC4 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZSC4 
Go to UniProtKB:  Q5ZSC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZSC4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BB2
Query on BB2

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
P [auth D]
ACTINONIN
C19 H35 N3 O5
XJLATMLVMSFZBN-VYDXJSESSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
N [auth C],
Q [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
O [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.65α = 90
b = 132.06β = 103.64
c = 90.38γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description