1I2C | pdb_00001i2c

CRYSTAL STRUCTURE OF MUTANT T145A SQD1 PROTEIN COMPLEX WITH NAD AND UDP-GLUCOSE

• PDB DOI: https://doi.org/10.2210/pdb1I2C/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-02-07 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: 1.60 Å
• R-Value Free: 
  0.185 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.177 (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: 46.9 kDa 
• Atom Count: 3,540 
• 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): 1  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: 1.60 Å
• R-Value Free:  0.185 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.177 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.682	α = 90
b = 159.682	β = 90
c = 99.038	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
CCP4	data reduction
CNS	refinement
CrystalClear	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: 2018-04-04
  Changes: Data collection
• Version 1.5: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.6: 2023-08-09
  Changes: Data collection, Refinement description