5V0P | pdb_00005v0p

Crystal Structure of Beta-ketoacyl-ACP synthase III-2 (FabH2) (C113A) from Vibrio Cholerae co-crystallized with octanoyl-CoA

• PDB DOI: https://doi.org/10.2210/pdb5V0P/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-02-28 Released: 2017-03-22 
• Deposition Author(s): Hou, J., Zheng, H., Cooper, D.R., Grabowski, M., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Beta-ketoacyl-ACP synthase III-2 (FabH2) (C113A) from Vibrio Cholerae co-crystallized with octanoyl-CoA

Hou, J., Zheng, H., Cooper, D.R., Chruszcz, M., Chordia, M.D., Grabowski, M., Minor, W.

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: 79.91 kDa 
• Atom Count: 5,809 
• Modeled Residue Count: 716 
• Deposited Residue Count: 724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2	A, B	362	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 1  Gene Names: fabH2, VC_A0751 EC: 2.3.1.180
UniProt
Find proteins for Q9KLJ3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KLJ3  Go to UniProtKB:  Q9KLJ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO8	D [auth A], F [auth B]	OCTANOYL-COENZYME A C29 H50 N7 O17 P3 S KQMZYOXOBSXMII-CECATXLMSA-N
NA	C [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35v0p

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.317	α = 90
b = 61.887	β = 93.18
c = 75.734	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Hou, J., Zheng, H., Cooper, D.R., Grabowski, M., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description