3O47 | pdb_00003o47

Crystal structure of ARFGAP1-ARF1 fusion protein

• PDB DOI: https://doi.org/10.2210/pdb3O47/pdb

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


• Deposited: 2010-07-26 Released: 2010-08-11 
• Deposition Author(s): Wang, H., Tong, Y., Nedyalkova, L., Tempel, W., Guan, X., Crombet, L., 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: 2.80 Å
• R-Value Free: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of ARFGAP1-ARF1 fusion protein

Wang, H., Tong, Y., Nedyalkova, L., Tempel, W., Guan, X., Crombet, L., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 76.91 kDa 
• Atom Count: 4,504 
• Modeled Residue Count: 578 
• Deposited Residue Count: 658 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor GTPase-activating protein 1, ADP-ribosylation factor 1	A, B	329	Homo sapiens	Mutation(s): 0  Gene Names: ARFGAP1, ARF1GAP, ARF1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P84077 (Homo sapiens) Explore P84077  Go to UniProtKB:  P84077
PHAROS:  P84077 GTEx:  ENSG00000143761
Find proteins for Q8N6T3 (Homo sapiens) Explore Q8N6T3  Go to UniProtKB:  Q8N6T3
PHAROS:  Q8N6T3 GTEx:  ENSG00000101199
UniProt Groups	P84077Q8N6T3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A], F [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.298	α = 90
b = 129.161	β = 90
c = 157.685	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-11 
Deposition Author(s): Wang, H., Tong, Y., Nedyalkova, L., Tempel, W., Guan, X., Crombet, L., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description