4X9O | pdb_00004x9o

Beta-ketoacyl-ACP synthase III -2 (FabH2) (C113A) from Vibrio Cholerae soaked with octanoyl-CoA: conformational changes without clearly bound substrate

• PDB DOI: https://doi.org/10.2210/pdb4X9O/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-12-11 Released: 2015-03-11 
• Deposition Author(s): Hou, J., Cooper, D.R., Shabalin, I.G., Grabowski, M., Shumilin, I., 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: 2.30 Å
• R-Value Free: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Structural and enzymatic studies of beta-ketoacyl-(acyl carrier protein) synthase III (FabH) from Vibrio cholerae

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

Macromolecule Content 

• Total Structure Weight: 78.07 kDa 
• Atom Count: 4,558 
• Modeled Residue Count: 642 
• 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34x9o

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.705	α = 90
b = 84.246	β = 90
c = 134.883	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-03-11 
Deposition Author(s): Hou, J., Cooper, D.R., Shabalin, I.G., Grabowski, M., Shumilin, I., 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	HHSN272200700058C

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2015-10-14
  Changes: Data collection
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence
• Version 1.4: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.5: 2023-09-27
  Changes: Data collection, Refinement description