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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diaminopimelate decarboxylase
A, B, C, D
427Psychromonas ingrahamii 37Mutation(s): 0 
Gene Names: lysAPing_0041
EC: 4.1.1.20
UniProt
Find proteins for A1SR00 (Psychromonas ingrahamii (strain DSM 17664 / CCUG 51855 / 37))
Explore A1SR00 
Go to UniProtKB:  A1SR00
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1SR00
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LLP
Query on LLP

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

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
M [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
U [auth C],
V [auth C],
Y [auth D]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
TME
Query on TME

Download Ideal Coordinates CCD File 
AA [auth D],
K [auth A],
Q [auth B],
R [auth B],
S [auth B]
PROPANE
C3 H8
ATUOYWHBWRKTHZ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
O [auth B]
P [auth B]
W [auth C]
I [auth A],
J [auth A],
O [auth B],
P [auth B],
W [auth C],
Z [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection