4XG1

Psychromonas ingrahamii diaminopimelate decarboxylase with LLP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

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 decarboxylaseA, B, C, D427Psychromonas ingrahamii 37Mutation(s): 0 
Gene Names: lysAPing_0041
EC: 4.1.1.20
Find proteins for A1SR00 (Psychromonas ingrahamii (strain 37))
Explore A1SR00 
Go to UniProtKB:  A1SR00
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LLP
Query on LLP

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

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A, B, C, D
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
TME
Query on TME

Download CCD File 
A, B, D
PROPANE
C3 H8
ATUOYWHBWRKTHZ-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.96α = 90
b = 103.13β = 94.77
c = 93.59γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
REFMACrefinement
Cootmodel building
XDSdata reduction
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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