5CX0 | pdb_00005cx0

Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv. oryzae, in complex with fragment 322

• PDB DOI: https://doi.org/10.2210/pdb5CX0/pdb

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


• Deposited: 2015-07-28 Released: 2016-08-03 
• Deposition Author(s): Ngo, H.P.T., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv. oryzae, in complex with fragment 322

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: 19.68 kDa 
• Atom Count: 1,344 
• Modelled Residue Count: 162 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
56L	F [auth A]	5-(propan-2-yl)-2-thioxodihydropyrimidine-4,6(1H,5H)-dione C7 H10 N2 O2 S QWVRNSPNBZGMRZ-UHFFFAOYSA-N
CD	B [auth A], C [auth A], D [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.751	α = 90
b = 58.751	β = 90
c = 266.092	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: 2024-03-20
  Changes: Data collection, Database references, Derived calculations