5E5D

Native structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv. oryzae

• PDB DOI: https://doi.org/10.2210/pdb5E5D/pdb
• Entry: 5E5D supersedes: 3DLD

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


• Deposited: 2015-10-08 Released: 2016-10-12 
• Deposition Author(s): Ngo, H.P.T., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3DLD

Literature

Native structure of Xoo1075, a peptide deformylase from Xanthomonas oryzae pv. oryzae

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: 24.17 kDa 
• Atom Count: 1,454 
• Modelled Residue Count: 170 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	212	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A], D [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.968	α = 90
b = 58.968	β = 90
c = 266.285	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: 2016-10-12 
Deposition Author(s): Ngo, H.P.T., Kang, L.W.
• This entry supersedes: 3DLD

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description