3PIT | pdb_00003pit

Crystal structure of M-RasD41E in complex with GppNHp (type 2)

• PDB DOI: https://doi.org/10.2210/pdb3PIT/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-11-08 Released: 2011-03-09 
• Deposition Author(s): Muraoka, S., Matsumoto, K., Shima, F., Hu, L., Ijiri, Y., Hirai, R., Liao, J., Kataoka, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.213 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of M-RasD41E in complex with GppNHp (type 2)

Muraoka, S., Matsumoto, K., Shima, F., Hu, L., Ijiri, Y., Hirai, R., Liao, J., Kataoka, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.4 kDa 
• Atom Count: 1,628 
• Modeled Residue Count: 168 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein M-Ras	A	183	Mus musculus	Mutation(s): 1  Gene Names: Mras, Xras EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for O08989 (Mus musculus) Explore O08989  Go to UniProtKB:  O08989
IMPC:  MGI:1100856

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.213 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.111	α = 90
b = 89.646	β = 90
c = 41.273	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-09 
Deposition Author(s): Muraoka, S., Matsumoto, K., Shima, F., Hu, L., Ijiri, Y., Hirai, R., Liao, J., Kataoka, T.

Revision History  

• Version 1.0: 2011-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description