3Q62 | pdb_00003q62

Crystal Structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb3Q62/pdb

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


• Deposited: 2010-12-30 Released: 2011-01-12 
• Deposition Author(s): Zhang, R., Maltseva, N., 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: 1.40 Å
• R-Value Free: 
  0.187 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Yersinia pestis

Zhang, R., Maltseva, N., Kwon, K., Anderson, W.F., Joachimiak, A., 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: 38.6 kDa 
• Atom Count: 3,264 
• Modelled Residue Count: 341 
• 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, YPTB1450 EC: 4.2.1.60 (PDB Primary Data), 5.3.3.14 (UniProt), 4.2.1.59 (UniProt)
UniProt
Find proteins for Q66CF3 (Yersinia pseudotuberculosis serotype I (strain IP32953)) Explore Q66CF3  Go to UniProtKB:  Q66CF3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A], D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.187 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33q62

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.433	α = 90
b = 50.668	β = 90
c = 132.384	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-12 
Deposition Author(s): Zhang, R., Maltseva, N., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description