4NT8 | pdb_00004nt8

Formyl-methionine-alanine complex structure of peptide deformylase from Xanthomoonas oryzae pv. oryzae

• PDB DOI: https://doi.org/10.2210/pdb4NT8/pdb

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


• Deposited: 2013-12-02 Released: 2014-12-03 
• Deposition Author(s): Ngo, H.P.T., Kim, J.K., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

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

Ngo, H.P.T., Kim, J.K., 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: 19.93 kDa 
• Atom Count: 1,444 
• Modeled Residue Count: 168 
• 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FME	H [auth A]	N-FORMYLMETHIONINE C6 H11 N O3 S PYUSHNKNPOHWEZ-YFKPBYRVSA-N
CD	B [auth A], C [auth A], D [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
GOL	J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ALA	I [auth A]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.584	α = 90
b = 58.584	β = 90
c = 266.188	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Ngo, H.P.T., Kim, J.K., Kang, L.W.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary