5KP2 | pdb_00005kp2

Beta-ketoacyl-ACP synthase III -2 (FabH2) (C113A) from Vibrio Cholerae cocrystallized with octanoyl-CoA: hydrolzed ligand

• PDB DOI: https://doi.org/10.2210/pdb5KP2/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2016-07-01 Released: 2016-07-20 
• Deposition Author(s): Hou, J., Zheng, H., Grabowski, M., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): Department of Health & Human Services (HHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Beta-ketoacyl-ACP synthase III -2 (FabH2) (C113A) from Vibrio Cholerae soaked with octanoyl-CoA: hydrolzed ligand

Center for Structural Genomics of Infectious Diseases (CSGID), Hou, J., Zheng, H., Grabowski, M., Anderson, W.F.

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: 78.98 kDa 
• Atom Count: 5,762 
• Modeled Residue Count: 715 
• 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
COA	C [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
OCA	D [auth B]	OCTANOIC ACID (CAPRYLIC ACID) C8 H16 O2 WWZKQHOCKIZLMA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35kp2

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.67	α = 90
b = 61.242	β = 94.67
c = 71.524	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Hou, J., Zheng, H., Grabowski, M., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
Department of Health & Human Services (HHS)	United States	HHSN272200700058C
Department of Health & Human Services (HHS)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2022-03-23
  Changes: Author supporting evidence, Data collection, Database references
• Version 1.3: 2022-04-13
  Changes: Structure summary
• Version 1.4: 2023-10-04
  Changes: Data collection, Refinement description