5WOL

Crystal structure of dihydrodipicolinate reductase DapB from Coxiella burnetii

• PDB DOI: https://doi.org/10.2210/pdb5WOL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Coxiella burnetii RSA 493
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-02 Released: 2017-08-16 
• Deposition Author(s): Stogios, P.J., Wawrzak, Z., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.218 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Crystal structure of dihydrodipicolinate reductase DapB from Coxiella burnetii

Stogios, P.J.

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)

Macromolecule Content

• Total Structure Weight: 28.08 kDa 
• Atom Count: 2,117 
• Modelled Residue Count: 230 
• Deposited Residue Count: 239 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate reductase	A	239	Coxiella burnetii RSA 493	Mutation(s): 0  Gene Names: dapB, CBU_1709 EC: 1.17.1.8
UniProt
Find proteins for P24703 (Coxiella burnetii (strain RSA 493 / Nine Mile phase I)) Explore P24703  Go to UniProtKB:  P24703

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
PE3	G [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C28 H58 O15 ILLKMACMBHTSHP-UHFFFAOYSA-N
6PC	E [auth A], F [auth A]	PYRIDINE-2-CARBOXYLIC ACID C6 H5 N O2 SIOXPEMLGUPBBT-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.218 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.605	α = 90
b = 78.795	β = 90
c = 84.074	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Stogios, P.J., Wawrzak, Z., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description