4RYB | pdb_00004ryb

Crystal structure of beta-ketoacyl-ACP synthase III (FabH) from Neisseria meningitidis

• PDB DOI: https://doi.org/10.2210/pdb4RYB/pdb

• Classification: TRANSFERASE
• Organism(s): Neisseria meningitidis FAM18
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-12-14 Released: 2014-12-31 
• Deposition Author(s): Nanson, J.D., Forwood, J.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of beta-ketoacyl-ACP synthase III (FabH) from Neisseria meningitidis

Nanson, J.D., Forwood, J.K.

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: 67.95 kDa 
• Atom Count: 4,835 
• Modeled Residue Count: 638 
• Deposited Residue Count: 640 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 3	A, B	320	Neisseria meningitidis FAM18	Mutation(s): 0  Gene Names: fabH EC: 2.3.1.180
UniProt
Find proteins for A1KRY9 (Neisseria meningitidis serogroup C / serotype 2a (strain ATCC 700532 / DSM 15464 / FAM18)) Explore A1KRY9  Go to UniProtKB:  A1KRY9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.29	α = 90
b = 96.36	β = 90
c = 193.02	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Nanson, J.D., Forwood, J.K.

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary