2OCB | pdb_00002ocb

Crystal structure of human RAB9B in complex with a GTP analogue

• PDB DOI: https://doi.org/10.2210/pdb2OCB/pdb

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


• Deposited: 2006-12-20 Released: 2007-01-02 
• Deposition Author(s): Hong, B., Shen, L., Walker, J.R., Tempel, W., 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: 
  0.253 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.223 (DCC) 

Starting Model: experimental

Literature

Crystal structure of human RAB9B in complex with a GTP analogue

Hong, B., Shen, L., Walker, J.R., Tempel, W., 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.

Macromolecule Content 

• Total Structure Weight: 21.11 kDa 
• Atom Count: 1,445 
• Modeled Residue Count: 173 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-9B	A	180	Homo sapiens	Mutation(s): 0  Gene Names: RAB9B, RAB9L EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP90 (Homo sapiens) Explore Q9NP90  Go to UniProtKB:  Q9NP90
PHAROS:  Q9NP90 GTEx:  ENSG00000123570

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.253 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.223 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.43	α = 90
b = 70.43	β = 90
c = 97.715	γ = 120

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: 2007-01-02 
Deposition Author(s): Hong, B., Shen, L., Walker, J.R., Tempel, W., 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: 2007-01-02
  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