4U8D | pdb_00004u8d

X-ray structure of Mg-bound human sorcin

• PDB DOI: https://doi.org/10.2210/pdb4U8D/pdb

• Classification: calcium binding protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-08-02 Released: 2015-08-26 
• Deposition Author(s): Fiorillo, A., Ilari, A., Colotti, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.249 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

INVESTIGATING THE CONFORMATIONAL CHANGES of SORCIN TO SHED LIGHT ON SIGNAL TRANSDUCTION IN THE APOPTOTIC PROCESS

Ilari, A., Fiorillo, A., Colotti, G.

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)

Macromolecule Content 

• Total Structure Weight: 43.56 kDa 
• Atom Count: 2,893 
• Modeled Residue Count: 344 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorcin	A, B	198	Homo sapiens	Mutation(s): 0  Gene Names: SRI
UniProt & NIH Common Fund Data Resources
Find proteins for P30626 (Homo sapiens) Explore P30626  Go to UniProtKB:  P30626
PHAROS:  P30626 GTEx:  ENSG00000075142

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.249 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.832	α = 90
b = 117.832	β = 90
c = 86.88	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
REFMAC	refinement
MOLREP	phasing
XSCALE	data scaling
XSCALE	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-26 
Deposition Author(s): Fiorillo, A., Ilari, A., Colotti, G.

Revision History  

• Version 1.0: 2015-08-26
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description