2J1L | pdb_00002j1l

Crystal Structure of Human Rho-related GTP-binding protein RhoD

• PDB DOI: https://doi.org/10.2210/pdb2J1L/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-08-14 Released: 2006-09-18 
• Deposition Author(s): Pike, A.C.W., Johansson, C., Gileadi, C., Niesen, F.H., Sobott, F., Schoch, G., Elkins, J., Smee, C., Gorrec, F., Watt, S., Bray, J., Turnbull, A.P., von Delft, F., Arrowsmith, C., Edwards, A., Weigelt, J., Sundstrom, M., Doyle, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.242 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Rho-Related GTP-Binding Protein Rhod

Pike, A.C.W., Johansson, C., Gileadi, C., Niesen, F.H., Sobott, F., Schoch, G., Elkins, J., Smee, C., Gorrec, F., Watt, S., Bray, J., Turnbull, A.P., von Delft, F., Arrowsmith, C., Edwards, A., Weigelt, J., Sundstrom, M., Doyle, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 24.48 kDa 
• Atom Count: 1,197 
• Modeled Residue Count: 157 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RHO-RELATED GTP-BINDING PROTEIN RHOD	A	214	Homo sapiens	Mutation(s): 0  EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for O00212 (Homo sapiens) Explore O00212  Go to UniProtKB:  O00212
PHAROS:  O00212 GTEx:  ENSG00000173156

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.242 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.811	α = 90
b = 66.81	β = 90
c = 103.921	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-18 
Deposition Author(s): Pike, A.C.W., Johansson, C., Gileadi, C., Niesen, F.H., Sobott, F., Schoch, G., Elkins, J., Smee, C., Gorrec, F., Watt, S., Bray, J., Turnbull, A.P., von Delft, F., Arrowsmith, C., Edwards, A., Weigelt, J., Sundstrom, M., Doyle, D.

Revision History  

• Version 1.0: 2006-09-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description