5XM5 | pdb_00005xm5

Crystal structure of Zinc binding protein ZinT at 1.49 Angstrom from E. coli

• PDB DOI: https://doi.org/10.2210/pdb5XM5/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-05-12 Released: 2017-05-31 
• Deposition Author(s): Chen, J., Wang, L., Guo, J., Xu, Y.
• Funding Organization(s): The National Natural Science Foundation of China, the Program for Liaoning Excellent Talents in University, the Fundamental Research Funds for the Central Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.234 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Zinc binding protein ZinT at 1.49 Angstrom from E. coli

Chen, J., Wang, L., Guo, J., Xu, Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.26 kDa 
• Atom Count: 3,551 
• Modeled Residue Count: 374 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal-binding protein ZinT	A, B	193	Escherichia coli K-12	Mutation(s): 0  Gene Names: zinT, yodA, b1973, JW1956
UniProt
Find proteins for P76344 (Escherichia coli (strain K12)) Explore P76344  Go to UniProtKB:  P76344

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], E [auth A], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	F [auth A], G [auth A], H [auth A], L [auth B], M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.234 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.021	α = 90
b = 65.724	β = 91.24
c = 73.532	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Chen, J., Wang, L., Guo, J., Xu, Y.

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Funding Organization	Location	Grant Number
The National Natural Science Foundation of China	China	31200556
the Program for Liaoning Excellent Talents in University	China	LJQ2015030
the Fundamental Research Funds for the Central Universities	China	DC201502020203

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Data collection
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary