1XJ0 | pdb_00001xj0

Crystal Structure of the GDP-bound form of the RasG60A mutant

• PDB DOI: https://doi.org/10.2210/pdb1XJ0/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2004-09-22 Released: 2005-05-10 
• Deposition Author(s): Nassar, N., Skowronek, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.239 (Depositor) 
• R-Value Work: 
  0.228 (Depositor) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Structure of an intermediate for nucleotide exchange by Ras

Nassar, N., Skowronek, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.4 kDa 
• Atom Count: 1,423 
• Modeled Residue Count: 166 
• Deposited Residue Count: 166 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming protein p21/H-Ras-1	A	166	Homo sapiens	Mutation(s): 2  Gene Names: HRAS, HRAS1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens) Explore P01112  Go to UniProtKB:  P01112
PHAROS:  P01112 GTEx:  ENSG00000174775

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.239 (Depositor) 
• R-Value Work:  0.228 (Depositor) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.64	α = 90
b = 93.64	β = 90
c = 121.56	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-10 
Deposition Author(s): Nassar, N., Skowronek, K.

Revision History  

• Version 1.0: 2005-05-10
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2021-10-20
  Changes: Atomic model, Database references, Derived calculations
• Version 2.1: 2023-08-23
  Changes: Data collection, Refinement description