6JKW

Seleno-methionine PNGM-1 from deep-sea sediment metagenome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report



Literature

PNGM 1 a novel subclass B3 metallo beta lactamase from a deep sea sediment metagenome

Kang, L.W.Lee, S.H.

(2018) J Glob Antimicrob Resist 14: 302-305

  • DOI: 10.1016/j.jgar.2018.05.021
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In order to find antimicrobial resistance gene(s) pre-dating the use of antibiotics through metagenomics, functional screening of a metagenomic library from the deep-seep sediments of Edison Seamount (ca. 10000 years old) was performed.

    In order to find antimicrobial resistance gene(s) pre-dating the use of antibiotics through metagenomics, functional screening of a metagenomic library from the deep-seep sediments of Edison Seamount (ca. 10000 years old) was performed.


    Organizational Affiliation

    National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Republic of Korea. Electronic address: sangheelee@mju.ac.kr.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metallo-beta-lactamases PNGM-1
A, B, C, D, E, F, G, H
372Acinetobacter baumanniiMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, C, D, E, F, G, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,D,E,F,G,HL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.857α = 90
b = 83.124β = 110.18
c = 162.833γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release