3DZ8 | pdb_00003dz8

Crystal structure of human Rab3B GTPase bound with GDP

• PDB DOI: https://doi.org/10.2210/pdb3DZ8/pdb

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


• Deposited: 2008-07-29 Released: 2008-08-12 
• Deposition Author(s): Shen, Y., Tong, Y., Sukumar, D., Tempel, W., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.251 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human Rab3B GTPase bound with GDP

Shen, Y., Tong, Y., Sukumar, D., Tempel, W., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.63 kDa 
• Atom Count: 1,462 
• Modeled Residue Count: 178 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-3B	A	191	Homo sapiens	Mutation(s): 0  Gene Names: RAB3B EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P20337 (Homo sapiens) Explore P20337  Go to UniProtKB:  P20337
PHAROS:  P20337 GTEx:  ENSG00000169213

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
UNX	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.251 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.969	α = 90
b = 50.875	β = 110.91
c = 73.553	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ARP/wARP	model building
Coot	model building
MolProbity	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Shen, Y., Tong, Y., Sukumar, D., Tempel, W., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description