2AQN | pdb_00002aqn

CU/ZN superoxide dismutase from neisseria meningitidis

• PDB DOI: https://doi.org/10.2210/pdb2AQN/pdb

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


• Deposited: 2005-08-18 Released: 2006-10-31 
• Deposition Author(s): DiDonato, M., Kassmann, C.J., Bruns, C.K., Cabelli, D.E., Cao, Z., Tabatabai, L.B., Kroll, J.S., Getzoff, E.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.190 (Depositor), 0.147 (DCC) 
• R-Value Work: 
  0.129 (Depositor), 0.133 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

Literature

CU/ZN superoxide dismutase from neisseria meningitidis

DiDonato, M., Kassmann, C.J., Bruns, C.K., Cabelli, D.E., Cao, Z., Tabatabai, L.B., Kroll, J.S., Getzoff, E.D.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.77 kDa 
• Atom Count: 4,025 
• Modeled Residue Count: 465 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B, C	164	Neisseria meningitidis	Mutation(s): 0  Gene Names: sodC EC: 1.15.1.1
UniProt
Find proteins for P57005 (Neisseria meningitidis serogroup A / serotype 4A (strain DSM 15465 / Z2491)) Explore P57005  Go to UniProtKB:  P57005

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A], H [auth B], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	F [auth A], L [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CU1	D [auth A], G [auth B], J [auth C]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.190 (Depositor), 0.147 (DCC) 
• R-Value Work:  0.129 (Depositor), 0.133 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.791	α = 90
b = 64.592	β = 125.93
c = 82.73	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-31 
Deposition Author(s): DiDonato, M., Kassmann, C.J., Bruns, C.K., Cabelli, D.E., Cao, Z., Tabatabai, L.B., Kroll, J.S., Getzoff, E.D.

Revision History  

• Version 1.0: 2006-10-31
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary