3GAN | pdb_00003gan

Crystal structure of gene product from Arabidopsis thaliana At3g22680 with bound suramin

• PDB DOI: https://doi.org/10.2210/pdb3GAN/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-17 Released: 2009-03-03 
• Deposition Author(s): Burgie, E.S., Bingman, C.A., Wesenberg, G.E., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.241 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of gene product from Arabidopsis thaliana At3g22680 with bound suramin

Burgie, E.S., Bingman, C.A., Wesenberg, G.E., Phillips Jr., G.N.

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.87 kDa 
• Atom Count: 1,186 
• Modeled Residue Count: 113 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein At3g22680	A	157	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At3g22680, At3g22680.1, MWI23.5, Q9LUJ3, Y3268_ARATH
UniProt
Find proteins for Q9LUJ3 (Arabidopsis thaliana) Explore Q9LUJ3  Go to UniProtKB:  Q9LUJ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SVR	B [auth A], C [auth A]	8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID C51 H40 N6 O23 S6 FIAFUQMPZJWCLV-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.241 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.381	α = 90
b = 58.381	β = 90
c = 90.287	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Burgie, E.S., Bingman, C.A., Wesenberg, G.E., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2023-09-06
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.4: 2023-11-22
  Changes: Data collection
• Version 1.5: 2024-11-06
  Changes: Structure summary