8D57 | pdb_00008d57

Crystal Structure of dihydrodipicolinate reductase from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb8D57/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-06-04 Released: 2022-06-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of dihydrodipicolinate reductase from Acinetobacter baumannii

Abendroth, J., Davies, D.R., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 180.07 kDa 
• Atom Count: 11,302 
• Modeled Residue Count: 1,602 
• Deposited Residue Count: 1,686 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate reductase	A, B, C, D, E, F	281	Acinetobacter baumannii	Mutation(s): 0  Gene Names: dapB, AB945B12_02229, ABUW_0039, ACX61_00190, C6N18_01125, FDN00_01175, FGL68_08535, GNY86_11650, HB367_13645, NCTC13421_00044 EC: 1.17.1.8
UniProt
Find proteins for B0VA26 (Acinetobacter baumannii (strain AYE)) Explore B0VA26  Go to UniProtKB:  B0VA26

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.8	α = 90
b = 79.8	β = 90
c = 519.13	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description