3QZ3 | pdb_00003qz3

The crystal structure of ferritin from Vibrio cholerae O1 biovar El Tor str. N16961

• PDB DOI: https://doi.org/10.2210/pdb3QZ3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-04 Released: 2011-03-23 
• Deposition Author(s): Tan, K., Mulligan, R., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.219 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of ferritin from Vibrio cholerae O1 biovar El Tor str. N16961

Tan, K., Mulligan, R., Hasseman, J., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 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 and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.11 kDa 
• Atom Count: 4,155 
• Modeled Residue Count: 492 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferritin	A, B, C	184	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC_0078 EC: 1.16.3.2
UniProt
Find proteins for Q9KVR1 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVR1  Go to UniProtKB:  Q9KVR1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth B], F [auth C], G [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.219 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33qz3

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.96	α = 90
b = 144.96	β = 90
c = 136.921	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-23 
Deposition Author(s): Tan, K., Mulligan, R., Hasseman, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-11-20
  Changes: Structure summary