4RV2 | pdb_00004rv2

Crystal Structure of (3R)-hydroxyacyl-ACP dehydratase HadAB hetero-dimer from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.284 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4RV2

This is version 1.2 of the entry. See complete history

Literature

Crystal structure of dehydratase component HadAB complex of mycobacterial FAS-II pathway.

Biswas, R.Dutta, A.Dutta, D.Hazra, D.Banerjee, D.R.Basak, A.Das, A.K.

(2015) Biochem Biophys Res Commun 458: 369-374

  • DOI: https://doi.org/10.1016/j.bbrc.2015.01.119
  • Primary Citation Related Structures: 
    4RV2

  • PubMed Abstract: 

    Fatty acid biosynthesis type II in mycobacteria delivers the fatty acids required for mycolic acid synthesis. The pathway employs a unique maoC like β-hydroxyacyl-ACP dehydratase HadAB or HadBC heterodimer in the third step of the elongation cycle. Here we report the crystal structure of the HadAB complex determined using a Pb-SIRAS method. Crystal structure aided with enzymatic study establishes the roles of HadA as a scaffolding component and HadB as a catalytic component together indispensable for the activity. The detailed structural analysis of HadAB in combination with MD simulation endorses the spatial orientation of the central hot-dog helix and the dynamic nature of its associated loop in regulation of substrate specificities in dehydratase/hydratase family enzymes.


  • Organizational Affiliation
    • Department of Biotechnology, Indian Institute of Technology, Kharagpur, Kharagpur 721302, India.

Macromolecule Content 

  • Total Structure Weight: 31.46 kDa 
  • Atom Count: 2,103 
  • Modeled Residue Count: 276 
  • Deposited Residue Count: 287 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UPF0336 protein MSMEG_1340/MSMEI_1302146Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_1340MSMEI_1302
UniProt
Find proteins for A0QS40 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QS40 
Go to UniProtKB:  A0QS40
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QS40
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
MaoC family protein141Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: MSMEG_1341MSMEI_1303
UniProt
Find proteins for A0QS41 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QS41 
Go to UniProtKB:  A0QS41
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QS41
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.284 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.216 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.368α = 90
b = 132.368β = 90
c = 132.368γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations