4G88

Crystal structure of OmpA peptidoglycan-binding domain from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb4G88/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-22 Released: 2013-07-24 
• Deposition Author(s): Lee, W.C., Song, J.H., Park, J.S., Kim, H.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.234 
• R-Value Work: 0.210 

Literature

Enantiomer-dependent amino acid binding affinity of OmpA-like domains from Acinetobacter baumannii peptidoglycan-associated lipoprotein and OmpA

Lee, W.C., Park, J.S., Song, J.H., Kim, S.I., Lee, J.C., Cheong, J., Kim, H.Y.

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 112.86 kDa 
• Atom Count: 8,558 
• Modelled Residue Count: 973 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein Omp38	A, B, C, D, E, F, G, H	123	Acinetobacter baumannii	Mutation(s): 0  Gene Names: omp38, ompA
UniProt
Find proteins for Q6RYW5 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore Q6RYW5  Go to UniProtKB:  Q6RYW5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
API	I [auth A], J [auth B], K [auth C], L [auth D], N [auth E], O [auth F], P [auth G], R [auth H]	2,6-DIAMINOPIMELIC ACID C7 H14 N2 O4 GMKMEZVLHJARHF-SYDPRGILSA-N
SRT	M [auth D], Q [auth G]	S,R MESO-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-XIXRPRMCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.234 
• R-Value Work: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.52	α = 90
b = 99.3	β = 105.95
c = 98.12	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Lee, W.C., Song, J.H., Park, J.S., Kim, H.Y.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations