5CY8 | pdb_00005cy8

Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv oryze, in complex with fragment 244

• PDB DOI: https://doi.org/10.2210/pdb5CY8/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Xanthomonas oryzae pv. oryzae KACC 10331
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-30 Released: 2016-08-03 
• Deposition Author(s): Ngo, H.P.T., Kang, L.W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv oryze, in complex with fragment 244

Ngo, H.P.T., Kang, L.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.71 kDa 
• Atom Count: 1,472 
• Modelled Residue Count: 170 
• Deposited Residue Count: 171 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	171	Xanthomonas oryzae pv. oryzae KACC 10331	Mutation(s): 0  Gene Names: def, XOO1075 EC: 3.5.1.88
UniProt
Find proteins for Q5H3Z2 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)) Explore Q5H3Z2  Go to UniProtKB:  Q5H3Z2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
56V	B [auth A]	(3R)-2,3-dihydro[1,3]thiazolo[3,2-a]benzimidazol-3-ol C9 H8 N2 O S NRTXRMKJTFAUEX-MRVPVSSYSA-N
CD	C [auth A], D [auth A], E [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.661	α = 90
b = 58.661	β = 90
c = 263.749	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Ngo, H.P.T., Kang, L.W.

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description