3V70 | pdb_00003v70

Crystal Structure of Human GTPase IMAP family member 1

• PDB DOI: https://doi.org/10.2210/pdb3V70/pdb
• Entry: 3V70 supersedes: 3LXW

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-12-20 Released: 2012-01-11 
• Deposition Author(s): Nedyalkova, L., Shen, Y., Tong, Y., Tempel, W., Mackenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Andrews, D.W., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.246 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human GTPase IMAP family member 1

Nedyalkova, L., Shen, Y., Tong, Y., Tempel, W., Mackenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Andrews, D.W., Park, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.38 kDa 
• Atom Count: 3,292 
• Modeled Residue Count: 428 
• Deposited Residue Count: 494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase IMAP family member 1	A, B	247	Homo sapiens	Mutation(s): 0  Gene Names: GIMAP1, IMAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWP7 (Homo sapiens) Explore Q8WWP7  Go to UniProtKB:  Q8WWP7
PHAROS:  Q8WWP7 GTEx:  ENSG00000213203

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.246 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.348	α = 90
b = 81.348	β = 90
c = 178.934	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-11 
Deposition Author(s): Nedyalkova, L., Shen, Y., Tong, Y., Tempel, W., Mackenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Andrews, D.W., Park, H., Structural Genomics Consortium (SGC)
• This entry supersedes: 3LXW

Revision History  

• Version 1.0: 2012-01-11
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description