2QJF | pdb_00002qjf

Crystal structure of ATP-sulfurylase domain of human PAPS synthetase 1

• PDB DOI: https://doi.org/10.2210/pdb2QJF/pdb

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


• Deposited: 2007-07-07 Released: 2008-11-11 
• Deposition Author(s): Sekulic, N., Lavie, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

ATP-sulfurylase domain of human bifunctional PAPS-synthetase oscillates between dimeric and monomeric forms

Sekulic, N., Paarmann, I., Konrad, M., Lavie, A.

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 (software)

Macromolecule Content 

• Total Structure Weight: 94.35 kDa 
• Atom Count: 7,017 
• Modeled Residue Count: 781 
• Deposited Residue Count: 810 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 1	A, B	405	Homo sapiens	Mutation(s): 0  Gene Names: PAPSS1, ATPSK1, PAPSS EC: 2.7.7.4 (PDB Primary Data), 2.7.1.25 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O43252 (Homo sapiens) Explore O43252  Go to UniProtKB:  O43252
PHAROS:  O43252 GTEx:  ENSG00000138801

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADX	D [auth A], F [auth B]	ADENOSINE-5'-PHOSPHOSULFATE C10 H14 N5 O10 P S IRLPACMLTUPBCL-KQYNXXCUSA-N
K	C [auth A], E [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.1	α = 90
b = 99.9	β = 113
c = 75.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
XDS	data reduction
XSCALE	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-11 
Deposition Author(s): Sekulic, N., Lavie, A.

Revision History  

• Version 1.0: 2008-11-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description