3TGV | pdb_00003tgv

Crystal structure of HutZ,the heme storsge protein from Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb3TGV/pdb

• Classification: HEME BINDING PROTEIN
• Organism(s): Vibrio cholerae O395
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-08-17 Released: 2012-08-22 
• Deposition Author(s): Liu, X., Gong, J., Wang, Z., Du, Q., Wei, T., Zhu, D., Huang, Y., Xu, S., Gu, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HutZ,the heme storsge protein from Vibrio cholerae

Liu, X., Gong, J., Wang, Z., Du, Q., Wei, T., Zhu, D., Huang, Y., Xu, S., Gu, L.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.77 kDa 
• Atom Count: 4,935 
• Modeled Residue Count: 568 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme-binding protein HutZ	A, B, C, D	148	Vibrio cholerae O395	Mutation(s): 1  Gene Names: hutZ EC: 1.14.99.58
UniProt
Find proteins for Q9KL41 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KL41  Go to UniProtKB:  Q9KL41

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEZ	E [auth B], F [auth B], G [auth C], H [auth D]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.063	α = 90
b = 80.063	β = 90
c = 125.835	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-22 
Deposition Author(s): Liu, X., Gong, J., Wang, Z., Du, Q., Wei, T., Zhu, D., Huang, Y., Xu, S., Gu, L.

Revision History  

• Version 1.0: 2012-08-22
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description