4XG1

Psychromonas ingrahamii diaminopimelate decarboxylase with LLP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Expression to crystallization of diaminopimelate decarboxylase from the psychrophile Psychromonas ingrahamii

Peverelli, M.G.Newman, J.Panjikar, S.Perugini, M.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diaminopimelate decarboxylase
A, B, C, D
427Psychromonas ingrahamii (strain 37)Mutation(s): 0 
Gene Names: lysA
EC: 4.1.1.20
Find proteins for A1SR00 (Psychromonas ingrahamii (strain 37))
Go to UniProtKB:  A1SR00
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

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Download CCD File 
A, B, C, D
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
LLP
Query on LLP

Download SDF File 
Download CCD File 
A, B, C, D
(2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid
N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE
C14 H22 N3 O7 P
YQSOQJORMNSDJL-QFULYMJESA-N
 Ligand Interaction
TME
Query on TME

Download SDF File 
Download CCD File 
A, B, D
PROPANE
C3 H8
ATUOYWHBWRKTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 89.960α = 90.00
b = 103.130β = 94.77
c = 93.590γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
Cootmodel building
REFMACrefinement
SHELXphasing
Auto-Rickshawphasing
Blu-Icedata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Data collection, Derived calculations