4PFM | pdb_00004pfm

SHEWANELLA BENTHICA DHDPS WITH LYSINE AND PYRUVATE

• PDB DOI: https://doi.org/10.2210/pdb4PFM/pdb

• Classification: LYASE
• Organism(s): Shewanella benthica KT99
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-30 Released: 2015-05-06 
• Deposition Author(s): Wubben, J.M., Paxman, J.J., Dogovski, C., Panjikar, S., Perugini, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.16 kDa 
• Atom Count: 4,774 
• Modeled Residue Count: 590 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate synthase	A, B	295	Shewanella benthica KT99	Mutation(s): 0  Gene Names: dapA, KT99_11964 EC: 4.3.3.7
UniProt
Find proteins for A9DKW4 (Shewanella benthica KT99) Explore A9DKW4  Go to UniProtKB:  A9DKW4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	H [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
LYS	C [auth A], D [auth A], G [auth B]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
GOL	E [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	F [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KPI	A, B	L-PEPTIDE LINKING	C9 H16 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.273	α = 90
b = 83.929	β = 90
c = 143.868	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Wubben, J.M., Paxman, J.J., Dogovski, C., Panjikar, S., Perugini, M.A.

Revision History  

• 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