4WXK | pdb_00004wxk

Crystal structure of a peptide deformylase from Haemophilus influenzae

• PDB DOI: https://doi.org/10.2210/pdb4WXK/pdb

• Classification: HYDROLASE
• Organism(s): Haemophilus influenzae 86-028NP
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-14 Released: 2015-11-18 
• Deposition Author(s): Kishor, C., Addlagatta, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a peptide deformylase from Haemophilus influenzae

Kishor, C., Addlagatta, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 77.03 kDa 
• Atom Count: 5,644 
• Modelled Residue Count: 659 
• Deposited Residue Count: 676 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A, B, C, D	169	Haemophilus influenzae 86-028NP	Mutation(s): 0  Gene Names: def, NTHI0725 EC: 3.5.1.88
UniProt
Find proteins for Q4QMV6 (Haemophilus influenzae (strain 86-028NP)) Explore Q4QMV6  Go to UniProtKB:  Q4QMV6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], H [auth B], J [auth C], L [auth D], M [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	E [auth A], G [auth B], I [auth C], K [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.036	α = 90
b = 80.961	β = 97.81
c = 98.586	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
DENZO	data scaling
MOLREP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Kishor, C., Addlagatta, A.

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description