5UEJ

1.30 A crystal structure of DapE enzyme from Neisseria meningitidis MC58

• PDB DOI: https://doi.org/10.2210/pdb5UEJ/pdb

• Classification: HYDROLASE
• Organism(s): Neisseria meningitidis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-02 Released: 2017-02-01 
• Deposition Author(s): Nocek, B., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.153 
• R-Value Work: 0.113 
• R-Value Observed: 0.115 

Literature

1.30 A crystal structure of DapE enzyme from Neisseria meningitidis MC58

Nocek, B., Heath, T., Becker, D., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 84.1 kDa 
• Atom Count: 7,052 
• Modelled Residue Count: 751 
• Deposited Residue Count: 768 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-diaminopimelate desuccinylase	A, B	384	Neisseria meningitidis	Mutation(s): 0  Gene Names: dapE, NMB1530 EC: 3.5.1.18
UniProt
Find proteins for Q9JYL2 (Neisseria meningitidis serogroup B (strain MC58)) Explore Q9JYL2  Go to UniProtKB:  Q9JYL2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], J [auth B], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], D [auth A], G [auth B], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.153 
• R-Value Work: 0.113 
• R-Value Observed: 0.115 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.767	α = 90
b = 88.644	β = 90
c = 133.402	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Nocek, B., Joachimiak, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2017-02-08
  Changes: Database references, Structure summary
• Version 1.2: 2017-08-23
  Changes: Data collection
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations