5KHL | pdb_00005khl

Crystal Structure of periplasmic Heme binding protein HutB of Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb5KHL/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Vibrio cholerae O395
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-06-15 Released: 2017-02-22 
• Deposition Author(s): Agarwal, S., Dey, S., Ghosh, B., Dasgupta, J.
• Funding Organization(s): DAE (BRNS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of periplasmic Heme binding protein HutB of Vibrio cholerae

Agarwal, S., Biswas, M., Dasgupta, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.96 kDa 
• Atom Count: 1,968 
• Modeled Residue Count: 257 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemin ABC transporter, periplasmic hemin-binding protein HutB	A [auth B]	271	Vibrio cholerae O395	Mutation(s): 0  Gene Names: hutB, VC0395_0324
UniProt
Find proteins for A0A0H3AE70 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H3AE70  Go to UniProtKB:  A0A0H3AE70

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.884	α = 90
b = 62.884	β = 90
c = 135.774	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data processing
SCALA	data scaling
PHASER	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Agarwal, S., Dey, S., Ghosh, B., Dasgupta, J.

---

Funding Organization	Location	Grant Number
DAE (BRNS)	India	2013/37B/26/brns

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description