8SJB | pdb_00008sjb

Crystal structure of Zn2+ bound calprotectin variant H87C

• PDB DOI: https://doi.org/10.2210/pdb8SJB/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., Rodriguez, A.M., 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: 1.74 Å
• R-Value Free: 
  0.197 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Zn2+ bound calprotectin

Perera, Y.R., Nassif, A.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 and generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 44.77 kDa 
• Atom Count: 3,313 
• Modeled Residue Count: 365 
• Deposited Residue Count: 374 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A8	A, B	88	Homo sapiens	Mutation(s): 4  Gene Names: S100A8, CAGA, CFAG, MRP8
UniProt & NIH Common Fund Data Resources
Find proteins for P05109 (Homo sapiens) Explore P05109  Go to UniProtKB:  P05109
PHAROS:  P05109 GTEx:  ENSG00000143546

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein S100-A9	C, D	99	Homo sapiens	Mutation(s): 2  Gene Names: S100A9, CAGB, CFAG, MRP14
UniProt & NIH Common Fund Data Resources
Find proteins for P06702 (Homo sapiens) Explore P06702  Go to UniProtKB:  P06702
PHAROS:  P06702 GTEx:  ENSG00000163220

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	G [auth A], J [auth B]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	E [auth A], F [auth A], H [auth B], I [auth B], L [auth C], M [auth C], N [auth D], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.197 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.436	α = 90
b = 76.935	β = 90
c = 106.793	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PHENIX	phasing
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., Rodriguez, A.M., 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