5F6R | pdb_00005f6r

Co-crystal Structure of 3-hydroxydecanoyl-(acyl carrier protein) Dehydratase from Yersinia pestis with 5-Benzoylpentanoic Acid

• PDB DOI: https://doi.org/10.2210/pdb5F6R/pdb

• Classification: LYASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2015-12-06 Released: 2015-12-23 
• Deposition Author(s): Maltseva, N., Kim, Y., Zhang, R., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Co-crystal Structure of 3-hydroxydecanoyl-(acyl carrier protein) Dehydratase from Yersinia pestis with 5-Benzoylpentanoic Acid

Maltseva, N., Kim, Y., Zhang, R., Kwon, K., Anderson, W.F., Joachimiak, A., 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: 38.72 kDa 
• Atom Count: 3,347 
• Modeled Residue Count: 345 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase	A, B	175	Yersinia pestis CO92	Mutation(s): 0  Gene Names: fabA, AK38_1122 EC: 4.2.1.59 (PDB Primary Data), 5.3.3.14 (UniProt)
UniProt
Find proteins for Q8ZG80 (Yersinia pestis) Explore Q8ZG80  Go to UniProtKB:  Q8ZG80

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5VO	C [auth A], E [auth B]	6-oxidanylidene-6-phenyl-hexanoic acid C12 H14 O3 AIEMSTCGCMIJTI-UHFFFAOYSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35f6r

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.982	α = 90
b = 54.885	β = 90
c = 102.866	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Maltseva, N., Kim, Y., Zhang, R., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description