4BKW | pdb_00004bkw

Crystal structure of the C-terminal region of human ZFYVE9

• PDB DOI: https://doi.org/10.2210/pdb4BKW/pdb

• Classification: RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-04-30 Released: 2013-05-15 
• Deposition Author(s): Williams, E., Krojer, T., Vollmar, M., Shrestha, L., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 
  0.247 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal Structure of the C-Terminal Region of Human Zfyve9

Williams, E.

(2013) Ph D Thesis 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.77 kDa 
• Atom Count: 3,781 
• Modeled Residue Count: 479 
• Deposited Residue Count: 531 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 9	A	531	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O95405 (Homo sapiens) Explore O95405  Go to UniProtKB:  O95405
PHAROS:  O95405 GTEx:  ENSG00000157077

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO	B [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free:  0.247 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.751	α = 90
b = 113.751	β = 90
c = 155.098	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Williams, E., Krojer, T., Vollmar, M., Shrestha, L., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Data collection
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other