5Z83

Crystal structure of GenB1 from Micromonospora echinospora in complex with PLP (internal aldimine)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Complete reconstitution of the diverse pathways of gentamicin B biosynthesis.

Ban, Y.H.Song, M.C.Hwang, J.Y.Shin, H.L.Kim, H.J.Hong, S.K.Lee, N.J.Park, J.W.Cha, S.S.Liu, H.W.Yoon, Y.J.

(2019) Nat. Chem. Biol. 15: 295-303


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-6' aminotransferase
A, B
437Micromonospora echinosporaMutation(s): 0 
Gene Names: gacK (genB1, gntW)
Find proteins for Q70KD9 (Micromonospora echinospora)
Go to UniProtKB:  Q70KD9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.140α = 90.00
b = 88.012β = 90.00
c = 116.140γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-01-30 
  • Released Date: 2019-01-16 
  • Deposition Author(s): Hong, S.K., Cha, S.S.

Funding OrganizationLocationGrant Number
Ministry of Oceans and FisheriesKorea, Republic Of--

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-01-30
    Type: Data collection, Database references
  • Version 1.2: 2019-02-27
    Type: Data collection, Database references