2O52 | pdb_00002o52

Crystal structure of human RAB4B in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb2O52/pdb

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


• Deposited: 2006-12-05 Released: 2006-12-19 
• Deposition Author(s): Zhu, H., Tempel, W., Wang, J., Shen, Y., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.269 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.216 (DCC) 

Starting Model: experimental

Literature

Crystal structure of human RAB4B in complex with GDP

Zhu, H., Tempel, W., Wang, J., Shen, Y., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.76 kDa 
• Atom Count: 2,676 
• Modeled Residue Count: 325 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-4B	A, B	200	Homo sapiens	Mutation(s): 0  Gene Names: RAB4B EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61018 (Homo sapiens) Explore P61018  Go to UniProtKB:  P61018
PHAROS:  P61018 GTEx:  ENSG00000167578

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A], H [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
BME	E [auth A], I [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
MG	C [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX	F [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.269 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.216 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.528	α = 90
b = 67.528	β = 90
c = 179.955	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: 2006-12-19 
Deposition Author(s): Zhu, H., Tempel, W., Wang, J., Shen, Y., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-12-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description