2IL1 | pdb_00002il1

Crystal structure of a predicted human GTPase in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb2IL1/pdb

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


• Deposited: 2006-10-02 Released: 2006-10-10 
• Deposition Author(s): Wang, J., Shen, Y., 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: 2.10 Å
• R-Value Free: 
  0.266 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.255 (DCC) 

Starting Model: experimental

Literature

Crystal structure of a predicted human GTPase in complex with GDP

Wang, J., Shen, Y., 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 and generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.44 kDa 
• Atom Count: 1,354 
• Modeled Residue Count: 163 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rab12	A	192	Homo sapiens	Mutation(s): 0  Gene Names: Rab12 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IQ22 (Homo sapiens) Explore Q6IQ22  Go to UniProtKB:  Q6IQ22
PHAROS:  Q6IQ22

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX	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: 2.10 Å
• R-Value Free:  0.266 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.255 (DCC) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.463	α = 90
b = 45.463	β = 90
c = 315.454	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data scaling
REFMAC	refinement
ARP/wARP	model building
MolProbity	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-10 
Deposition Author(s): Wang, J., Shen, Y., 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: 2006-10-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, 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