3JZY | pdb_00003jzy

Crystal structure of human Intersectin 2 C2 domain

• PDB DOI: https://doi.org/10.2210/pdb3JZY/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-24 Released: 2009-10-06 
• Deposition Author(s): Shen, Y., Tempel, W., Tong, Y., Li, Y., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human Intersectin 2 C2 domain

Shen, Y., Tempel, W., Tong, Y., Li, Y., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.1 kDa 
• Atom Count: 1,151 
• Modeled Residue Count: 124 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intersectin 2	A	510	Homo sapiens	Mutation(s): 0  Gene Names: ITSN2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZM3 (Homo sapiens) Explore Q9NZM3  Go to UniProtKB:  Q9NZM3
PHAROS:  Q9NZM3 GTEx:  ENSG00000198399

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.125	α = 90
b = 54.125	β = 90
c = 196.709	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
Coot	model building
MolProbity	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Shen, Y., Tempel, W., Tong, Y., Li, Y., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2023-09-06
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description