4G4W | pdb_00004g4w

Crystal structure of peptidoglycan-associated lipoprotein from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb4G4W/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Acinetobacter baumannii TCDC-AB0715
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-16 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: 1.90 Å
• R-Value Free: 
  0.229 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 13.19 kDa 
• Atom Count: 959 
• Modeled Residue Count: 108 
• Deposited Residue Count: 114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan-associated lipoprotein	A	114	Acinetobacter baumannii TCDC-AB0715	Mutation(s): 0  Gene Names: ABTW07_3009, pal
UniProt
Find proteins for A0ABX6CIM9 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore A0ABX6CIM9  Go to UniProtKB:  A0ABX6CIM9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ALA	B [auth A]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.229 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.14	α = 90
b = 54.14	β = 90
c = 114.03	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 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations