6C87 | pdb_00006c87

Crystal structure of rab gdp dissociation inhibitor alpha from Naegleria fowleri

• PDB DOI: https://doi.org/10.2210/pdb6C87/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Naegleria fowleri
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-01-24 Released: 2018-02-14 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of rab gdp dissociation inhibitor alpha from Naegleria fowleri

Abendroth, J., Davies, D.R., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 204.98 kDa 
• Atom Count: 13,820 
• Modeled Residue Count: 1,765 
• Deposited Residue Count: 1,808 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rab GDP dissociation inhibitor alpha	A, B, C, D	452	Naegleria fowleri	Mutation(s): 0  Gene Names: NF0049320
UniProt
Find proteins for A0A2R2JFX6 (Naegleria fowleri) Explore A0A2R2JFX6  Go to UniProtKB:  A0A2R2JFX6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M36C87

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.34	α = 90
b = 103.12	β = 90
c = 195.55	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
SIMBAD	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2018-03-21
  Changes: Refinement description
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description