7JPJ

Crystal Structure of the essential dimeric LYSA from Phaeodactylum tricornutum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The Phaeodactylum tricornutum diaminopimelate decarboxylase was acquired via horizontal gene transfer from bacteria and displays substrate promiscuity

Bielinski, V.A.Brunson, J.K.Ghosh, A.Moosburner, M.A.Garza, E.A.Fussy, Z.Bai, J.McKinnie, S.M.K.Moore, B.S.Allen, A.E.Almo, S.C.Dupont, C.L.

(2020) bioRxiv 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diaminopimelate decarboxylase
A, B
441Phaeodactylum tricornutum CCAP 1055/1Mutation(s): 0 
Gene Names: PHATRDRAFT_21592
UniProt
Find proteins for B7G3A2 (Phaeodactylum tricornutum (strain CCAP 1055/1))
Explore B7G3A2 
Go to UniProtKB:  B7G3A2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7G3A2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DLY (Subject of Investigation/LOI)
Query on DLY

Download Ideal Coordinates CCD File 
C [auth A]D-LYSINE
C6 H14 N2 O2
KDXKERNSBIXSRK-RXMQYKEDSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth B]
H [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth B],
H [auth B],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.78α = 90
b = 86.324β = 90
c = 127.196γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description