5XW2

Crystal structure of the Hydroxylase HmtN in C 1 2 1 crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

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This is version 1.1 of the entry. See complete history


Literature

Molecular characterization of the hydroxylase HmtN at 1.3 angstrom resolution.

Zhang, H.Chen, J.Zhang, H.

(2017) Biochem Biophys Res Commun 

  • DOI: https://doi.org/10.1016/j.bbrc.2017.07.010
  • Primary Citation of Related Structures:  
    5XW2

  • PubMed Abstract: 

    Himastatin is a novel antibiotic with antitumor and antibacterial activity. In the himastatin biosynthesis pathway, HmtN is responsible for the hydroxylation of the piperazic acid (Pip) motif. Herein, we present the crystal structures of HmtN (1.3 Å), which is the first structure for a cytochrome P450 involved in the hydroxylation of cyclohexadepsipeptide during himastatin biosynthesis. Structure analysis indicated that almost all the surface of HmtN has negative electrostatic potential, only small patches of positive electrostatic potential can be found. It is worth noting that almost the entire active site of HmtT is negatively charged, while HmtN active site is composed of positive and negative charge. This may be relevant to their specific substrate recognition and different catalytic function. In addition, three channels were observed in HmtN crystal structure; channel 3 may be essential for substrate ingress and egress from the active site to the surface, while channel 1 and channel 2 may be the solvent and water pathway, respectively.


  • Organizational Affiliation

    Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiao Hong Shan No.44, Wuhan 430071, China. Electronic address: huaidongzhang@yahoo.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 107B1 (P450CVIIB1)419Streptomyces himastatinicus ATCC 53653Mutation(s): 0 
Gene Names: hmtNSSOG_07636
UniProt
Find proteins for D9WMQ6 (Streptomyces himastatinicus ATCC 53653)
Explore D9WMQ6 
Go to UniProtKB:  D9WMQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9WMQ6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.13α = 90
b = 72.84β = 107.43
c = 53.75γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description