4BFC | pdb_00004bfc

Crystal structure of the C-terminal CMP-Kdo binding domain of WaaA from Acinetobacter baumannii

• PDB DOI: https://doi.org/10.2210/pdb4BFC/pdb

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


• Deposited: 2013-03-18 Released: 2014-04-02 
• Deposition Author(s): Kimbung, Y.R., Hakansson, M., Logan, D., Wang, P.F., Schulz, M., Mamat, U., Woodard, R.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.161 (Depositor), 0.153 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.132 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the C-Terminal Cmp-Kdo Binding Domain of Waaa from Acinetobacter Baumannii

Kimbung, Y.R., Hakansson, M., Logan, D., Wang, P.F., Schulz, M., Mamat, U., Woodard, R.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 27.03 kDa 
• Atom Count: 1,776 
• Modeled Residue Count: 193 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-DEOXY-D-MANNO-OCTULOSONIC-ACID TRANSFERASE	A	235	Acinetobacter baumannii	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	C [auth A], D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.161 (Depositor), 0.153 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.132 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.37	α = 90
b = 110.37	β = 90
c = 70.34	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Kimbung, Y.R., Hakansson, M., Logan, D., Wang, P.F., Schulz, M., Mamat, U., Woodard, R.W.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2015-04-08
  Changes: Structure summary
• Version 1.2: 2018-01-17
  Changes: Advisory, Data collection
• Version 1.3: 2023-12-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description