2GF0 | pdb_00002gf0

The crystal structure of the human DiRas1 GTPase in the inactive GDP bound state

• PDB DOI: https://doi.org/10.2210/pdb2GF0/pdb

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


• Deposited: 2006-03-21 Released: 2006-04-04 
• Deposition Author(s): Turnbull, A.P., Papagrigoriou, E., Yang, X., Schoch, G., Elkins, J., Gileadi, O., Salah, E., Bray, J., Wen-Hwa, L., Fedorov, O., Niesen, F.E., von Delft, F., Weigelt, J., Edwards, A., Arrowsmith, C., Sundstrom, M., Doyle, D., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.208 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of the human DiRas1 GTPase in the inactive GDP bound state

Turnbull, A.P., Papagrigoriou, E., Yang, X., Schoch, G., Elkins, J., Gileadi, O., Salah, E., Bray, J., Wen-Hwa, L., Fedorov, O., Niesen, F.E., von Delft, F., Weigelt, J., Edwards, A., Arrowsmith, C., Sundstrom, M., Doyle, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 91.65 kDa 
• Atom Count: 6,183 
• Modeled Residue Count: 688 
• Deposited Residue Count: 796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein Di-Ras1	A, B, C, D	199	Homo sapiens	Mutation(s): 0  Gene Names: DIRAS1, GBTS1, RIG
UniProt & NIH Common Fund Data Resources
Find proteins for O95057 (Homo sapiens) Explore O95057  Go to UniProtKB:  O95057
PHAROS:  O95057 GTEx:  ENSG00000176490

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	F [auth A], H [auth B], J [auth C], L [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	E [auth A], G [auth B], I [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.208 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.053	α = 90
b = 94.031	β = 89.98
c = 61.214	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-04 
Deposition Author(s): Turnbull, A.P., Papagrigoriou, E., Yang, X., Schoch, G., Elkins, J., Gileadi, O., Salah, E., Bray, J., Wen-Hwa, L., Fedorov, O., Niesen, F.E., von Delft, F., Weigelt, J., Edwards, A., Arrowsmith, C., Sundstrom, M., Doyle, D., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-04-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description