8SJC

Crystal structure of Zn2+ bound calprotectin

• PDB DOI: https://doi.org/10.2210/pdb8SJC/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-04-17 Released: 2024-07-03 
• Deposition Author(s): Perera, Y.R., Garcia, V., Guillen, R.M., Chazin, W.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.197 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Starting Model: experimental

Literature

Crystal structure of Zn2+ bound calprotectin

Perera, Y.R., Garcia, V., Guillen, R.M., Chazin, W.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 46.17 kDa 
• Atom Count: 3,468 
• Modelled Residue Count: 385 
• Deposited Residue Count: 390 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A8	A, B	87	Homo sapiens	Mutation(s): 1  Gene Names: S100A8, CAGA, CFAG, MRP8
UniProt & NIH Common Fund Data Resources
Find proteins for P05109 (Homo sapiens) Explore P05109  Go to UniProtKB:  P05109
GTEx:  ENSG00000143546

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A9	C, D	108	Homo sapiens	Mutation(s): 0  Gene Names: S100A9, CAGB, CFAG, MRP14
UniProt & NIH Common Fund Data Resources
Find proteins for P06702 (Homo sapiens) Explore P06702  Go to UniProtKB:  P06702
GTEx:  ENSG00000163220

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	E [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	O [auth C], R [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	F [auth A], G [auth A], I [auth B], K [auth C], L [auth C], M [auth C], N [auth C], P [auth D], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	H [auth B], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.197 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.611	α = 90
b = 114.611	β = 90
c = 53.182	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
Coot	model building
PHENIX	refinement
HKL-2000	data reduction
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Perera, Y.R., Garcia, V., Guillen, R.M., Chazin, W.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 AI127793
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	AI101171

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release