5HA4 | pdb_00005ha4

Structure of a diaminopimelate epimerase from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb5HA4/pdb

• Classification: ISOMERASE
• Organism(s): Acinetobacter baumannii AB307-0294
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-12-30 Released: 2016-01-27 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.190 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Structure of a diaminopimelate epimerase from Acinetobacter baumannii

Mayclin, S.J., Lorimer, D.D., Edwards, T.E.

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)

Macromolecule Content 

• Total Structure Weight: 63.09 kDa 
• Atom Count: 4,949 
• Modeled Residue Count: 562 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate epimerase	A, B	282	Acinetobacter baumannii AB307-0294	Mutation(s): 0  Gene Names: dapF, ABBFA_000848 EC: 5.1.1.7
UniProt
Find proteins for B7GY71 (Acinetobacter baumannii (strain AB307-0294)) Explore B7GY71  Go to UniProtKB:  B7GY71

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	C [auth A], D [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
CL	E [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.190 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35HA4

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.38	α = 90
b = 96.18	β = 90
c = 106.24	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary