1I24 | pdb_00001i24

HIGH RESOLUTION CRYSTAL STRUCTURE OF THE WILD-TYPE PROTEIN SQD1, WITH NAD AND UDP-GLUCOSE

• PDB DOI: https://doi.org/10.2210/pdb1I24/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-02-05 Released: 2003-07-01 
• Deposition Author(s): Theisen, M.J., Sanda, S.L., Ginell, S.L., Benning, C., Garavito, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.198 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Characterization of the Active Site of Udp-Sulfoquinovose Synthase: Formation of the Sulfonic Acid Product in the Crystalline State

Theisen, M.J., Sanda, S.L., Ginell, S.L., Benning, C., Garavito, R.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.93 kDa 
• Atom Count: 3,622 
• Modeled Residue Count: 393 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SULFOLIPID BIOSYNTHESIS PROTEIN SQD1	A	404	Arabidopsis thaliana	Mutation(s): 0  Gene Names: SQD1 EC: 3.13.1.1
UniProt
Find proteins for O48917 (Arabidopsis thaliana) Explore O48917  Go to UniProtKB:  O48917

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
UPG	E [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.198 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.243	α = 90
b = 160.243	β = 90
c = 99.273	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
HKL-2000	data collection
SCALEPACK	data scaling
TRUNCATE	data reduction
CNS	refinement
d*TREK	data reduction
HKL-2000	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-01 
Deposition Author(s): Theisen, M.J., Sanda, S.L., Ginell, S.L., Benning, C., Garavito, R.M.

Revision History  

• Version 1.0: 2003-07-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description