2A5J | pdb_00002a5j

Crystal Structure of Human RAB2B

• PDB DOI: https://doi.org/10.2210/pdb2A5J/pdb

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


• Deposited: 2005-06-30 Released: 2005-07-19 
• Deposition Author(s): Dong, A., Wang, J., Shen, Y., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Bochkarev, A., Park, H.W., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.225 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human RAB2B

Wang, J., Dong, A., Shen, Y., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Bochkarev, A., Park, H.W.

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: 22.22 kDa 
• Atom Count: 1,717 
• Modeled Residue Count: 177 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-2B	A	191	Homo sapiens	Mutation(s): 0  EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUD1 (Homo sapiens) Explore Q8WUD1  Go to UniProtKB:  Q8WUD1
PHAROS:  Q8WUD1 GTEx:  ENSG00000129472

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.225 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.104	α = 90
b = 54.732	β = 90
c = 70.765	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-19 
Deposition Author(s): Dong, A., Wang, J., Shen, Y., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Bochkarev, A., Park, H.W., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2005-07-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description