5XR7 | pdb_00005xr7

Crystal structure of RabA1a (Q72K) in complex with GTP

• PDB DOI: https://doi.org/10.2210/pdb5XR7/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-06-07 Released: 2018-06-13 
• Deposition Author(s): Yun, J.S., Chang, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.285 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Crystal structure and subcellular localization of RabA1a from Arabidopsis thaliana

Yun, J.S., Ha, S.C., Kim, Y.G., Kim, H.R., Chang, J.H.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.75 kDa 
• Atom Count: 2,691 
• Modeled Residue Count: 333 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein RABA1a	A, B	194	Arabidopsis thaliana	Mutation(s): 1  Gene Names: RABA1A, ARA-2, RAB11E, At1g06400, T2D23.10, T2D23_5
UniProt
Find proteins for P28185 (Arabidopsis thaliana) Explore P28185  Go to UniProtKB:  P28185

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	C [auth A], E [auth B]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.285 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.57	α = 86.66
b = 43.046	β = 74.07
c = 67.609	γ = 82.28

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Yun, J.S., Chang, J.H.

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Derived calculations