3KH0 | pdb_00003kh0

Crystal structure of the Ras-association (RA) domain of RALGDS

• PDB DOI: https://doi.org/10.2210/pdb3KH0/pdb

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


• Deposited: 2009-10-29 Released: 2009-11-17 
• Deposition Author(s): Shen, Y., Tempel, W., Wang, H., Tong, Y., 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: 2.10 Å
• R-Value Free: 
  0.226 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Ras-association (RA) domain of RALGDS

Shen, Y., Tempel, W., Wang, H., Tong, Y., 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 assigned by authors.

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: 32.05 kDa 
• Atom Count: 1,671 
• Modelled Residue Count: 207 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ral guanine nucleotide dissociation stimulator	A, B	140	Homo sapiens	Mutation(s): 0  Gene Names: RALGDS, KIAA1308, RGF
UniProt & NIH Common Fund Data Resources
Find proteins for Q12967 (Homo sapiens) Explore Q12967  Go to UniProtKB:  Q12967
PHAROS:  Q12967 GTEx:  ENSG00000160271

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.226 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.59	α = 90
b = 104.59	β = 90
c = 39.819	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Shen, Y., Tempel, W., Wang, H., Tong, Y., 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: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description