4JRM | pdb_00004jrm

Crystal structure of beta-ketoacyl-ACP synthase II (FabF) from Vibrio Cholerae (space group P212121) at 1.75 Angstrom

• PDB DOI: https://doi.org/10.2210/pdb4JRM/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-21 Released: 2013-04-03 
• Deposition Author(s): Hou, J., Chruszcz, M., Shabalin, I.G., Zheng, H., Cooper, D.R., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.231 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of beta-ketoacyl-ACP synthase II (FabF) from Vibrio cholerae (space group P43) at 2.2 Angstrom

Hou, J., Chruszcz, M., Shabalin, I.G., Zheng, H., Cooper, D.R., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Macromolecule Content 

• Total Structure Weight: 174.41 kDa 
• Atom Count: 12,748 
• Modeled Residue Count: 1,649 
• Deposited Residue Count: 1,668 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 2	A [auth D], B [auth A], C [auth B], D [auth C]	417	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: fabF, VC2019, VC_2019 EC: 2.3.1.179
UniProt
Find proteins for Q9KQH9 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQH9  Go to UniProtKB:  Q9KQH9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	E [auth D], G [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.231 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34jrm

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.543	α = 90
b = 136.376	β = 90
c = 168.478	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Hou, J., Chruszcz, M., Shabalin, I.G., Zheng, H., Cooper, D.R., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Refinement description