4PFM

SHEWANELLA BENTHICA DHDPS WITH LYSINE AND PYRUVATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Defining a Molecular Determinant of Lysine-Mediated Allosteric Inhibition of DHDPS.

Wubben, J.M.Paxman, J.J.Dogovski, C.Panjikar, S.Perugini, M.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxy-tetrahydrodipicolinate synthase
A, B
295Shewanella benthica KT99Mutation(s): 0 
Gene Names: dapAKT99_11964
EC: 4.3.3.7
UniProt
Find proteins for A9DKW4 (Shewanella benthica KT99)
Explore A9DKW4 
Go to UniProtKB:  A9DKW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9DKW4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
H [auth B]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
LYS
Query on LYS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KPI
Query on KPI
A, B
L-PEPTIDE LINKINGC9 H16 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.273α = 90
b = 83.929β = 90
c = 143.868γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Advisory, Data collection, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-11-29
    Changes: Data collection