3IQ1 | pdb_00003iq1

Crystal structure of DPS protein from Vibrio cholerae O1, a member of a broad superfamily of ferritin-like diiron-carboxylate proteins

• PDB DOI: https://doi.org/10.2210/pdb3IQ1/pdb

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


• Deposited: 2009-08-18 Released: 2009-09-08 
• Deposition Author(s): Nocek, B., Peterson, S., Gu, M., Otwinowski, Z., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.174 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Literature

Crystal structure of DPS protein from Vibrio cholerae O1, a member of a broad superfamily of ferritin-like diiron-carboxylate proteins

Nocek, B., Peterson, S., Gu, M., Otwinowski, Z., Anderson, W., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 73.93 kDa 
• Atom Count: 5,993 
• Modeled Residue Count: 631 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DPS family protein	A, B, C, D	159	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC_0139
UniProt
Find proteins for Q9KVK4 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KVK4  Go to UniProtKB:  Q9KVK4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth B], G [auth C], H [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.174 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33iq1

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.816	α = 90
b = 93.816	β = 90
c = 225.561	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
Coot	model building
MLPHARE	phasing
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Nocek, B., Peterson, S., Gu, M., Otwinowski, Z., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary