6MFD

GphF GNAT-like decarboxylase in complex with isobutyryl-CoA

  • Classification: LYASE
  • Organism(s): Archangium violaceum
  • Expression System: Escherichia coli BL21(DE3)

  • Deposited: 2018-09-10 Released: 2019-09-18 
  • Deposition Author(s): Skiba, M.A., Tran, C.L., Smith, J.L.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK); National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS); National Institutes of Health/National Cancer Institute (NIH/NCI) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.794 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

GphF GNAT-like decarboxylase in complex with isobutyryl-CoA

Skiba, M.A.Tran, C.L.Sikkema, A.P.Klaver, Z.Gerwick, W.H.Sherman, D.H.Smith, J.L.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GphF
B, A
232Archangium violaceumMutation(s): 0 
Gene Names: gphF
Find proteins for U6BSB2 (Archangium violaceum)
Go to UniProtKB:  U6BSB2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CO6
Query on CO6

Download SDF File 
Download CCD File 
A, B
ISOBUTYRYL-COENZYME A
IB-CO6
C25 H42 N7 O17 P3 S
AEWHYWSPVRZHCT-NDZSKPAWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.794 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.243 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 134.427α = 90.00
b = 145.473β = 90.00
c = 77.246γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK042303
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM008353
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA108874

Revision History 

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-12-04
    Type: Author supporting evidence