2ZKL | pdb_00002zkl

Crystal Structure of capsular polysaccharide assembling protein CapF from staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb2ZKL/pdb

• Classification: ISOMERASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-25 Released: 2009-03-31 
• Deposition Author(s): Miyafusa, T., Tanaka, Y., Yao, M., Tanaka, I., Tsumoto, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Literature

Crystal structure of capsular polysaccharide assembling protein from Staphylococcus aureus

Miyafusa, T., Tanaka, Y., Kuroda, M., Yao, M., Watanabe, N., Ohta, T., Tanaka, I., Tsumoto, K.

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)

Macromolecule Content 

• Total Structure Weight: 42.49 kDa 
• Atom Count: 2,940 
• Modeled Residue Count: 361 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsular polysaccharide synthesis enzyme Cap5F	A	369	Staphylococcus aureus	Mutation(s): 0  Gene Names: capF
UniProt
Find proteins for A0A0H3JP37 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JP37  Go to UniProtKB:  A0A0H3JP37

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.636	α = 90
b = 119.636	β = 90
c = 129.454	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ugiui	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-31 
Deposition Author(s): Miyafusa, T., Tanaka, Y., Yao, M., Tanaka, I., Tsumoto, K.

Revision History  

• Version 1.0: 2009-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations