4X9K | pdb_00004x9k

Beta-ketoacyl-acyl carrier protein synthase III-2 (FabH2)(C113A) from Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb4X9K/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: 2014-12-24 
• Deposition Author(s): Hou, J., Chruszcz, M., Zheng, H., Grabowski, M., Chordia, M.D., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.176 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

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

Hou, J., Chruszcz, M., Zheng, H., Grabowski, M., Chordia, M.D., Anderson, W.F., 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: 39.25 kDa 
• Atom Count: 3,167 
• Modeled Residue Count: 358 
• Deposited Residue Count: 362 
• 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	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	D [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.176 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34x9k

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.459	α = 90
b = 61.521	β = 90
c = 69.676	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: 2014-12-24 
Deposition Author(s): Hou, J., Chruszcz, M., Zheng, H., Grabowski, M., Chordia, M.D., 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 General Medical Sciences (NIH/NIGMS)	United States	HHSN272200700058C

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2015-01-07
  Changes: Database references, Structure summary
• Version 1.2: 2015-10-14
  Changes: Data collection
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2023-09-27
  Changes: Data collection, Refinement description