5UD6 | pdb_00005ud6

Crystal structure of DHDPS from Cyanidioschyzon merolae with lysine bound

• PDB DOI: https://doi.org/10.2210/pdb5UD6/pdb

• Classification: LYASE
• Organism(s): Cyanidioschyzon merolae strain 10D
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-12-23 Released: 2017-12-27 
• Deposition Author(s): Watkin, S., Keown, J.R., Pearce, F.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Crystal structure of DHDPS from Cyanidioschyzon merolae with lysine bound

Watkin, S., Keown, J.R., Pearce, F.G.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 141.82 kDa 
• Atom Count: 9,135 
• Modeled Residue Count: 1,194 
• Deposited Residue Count: 1,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B, C, D	327	Cyanidioschyzon merolae strain 10D	Mutation(s): 0  Gene Names: CYME_CME179C EC: 4.3.3.7
UniProt
Find proteins for M1V4H9 (Cyanidioschyzon merolae (strain NIES-3377 / 10D)) Explore M1V4H9  Go to UniProtKB:  M1V4H9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS	F [auth A], H [auth B], J [auth C], L [auth D]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
CA	E [auth A], G [auth B], I [auth C], K [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.63	α = 90
b = 74.7	β = 103.31
c = 97.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
iMOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-27 
Deposition Author(s): Watkin, S., Keown, J.R., Pearce, F.G.

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2018-12-05
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2025-04-02
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary