6LM2 | pdb_00006lm2

Crystal structure of Zinc binding protein ZinT from E. coli

• PDB DOI: https://doi.org/10.2210/pdb6LM2/pdb

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


• Deposited: 2019-12-24 Released: 2020-07-08 
• Deposition Author(s): Xiang, L., Zhang, G., Zhou, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Zinc binding protein ZinT from E. coli

Xiang, L., Zhang, G., Zhou, J.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.82 kDa 
• Atom Count: 1,544 
• Modeled Residue Count: 184 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal-binding protein ZinT	A	184	Escherichia coli 'BL21-Gold(DE3)pLysS AG	Mutation(s): 0
UniProt
Find proteins for P76344 (Escherichia coli (strain K12)) Explore P76344  Go to UniProtKB:  P76344

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.81	α = 90
b = 55.81	β = 90
c = 153.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Xiang, L., Zhang, G., Zhou, J.

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary