6REM | pdb_00006rem

Crystal structure of Pizza6-SH with Sulphate ion

• PDB DOI: https://doi.org/10.2210/pdb6REM/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-04-12 Released: 2020-05-13 
• Deposition Author(s): Noguchi, H., Clarke, D.E., Gryspeerdt, J.L., Feyter, S.D., Voet, A.R.D.
• Funding Organization(s): Research Foundation - Flanders

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Artificial beta-Propeller Protein-based Hydrolases

Noguchi, H., Clarke, D.E., Gryspeerdt, J.L., Feyter, S.D., Voet, A.R.D.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.45 kDa 
• Atom Count: 2,122 
• Modeled Residue Count: 251 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pizza6-SH	A	256	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [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:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.007	α = 90
b = 56.732	β = 90
c = 69.783	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Noguchi, H., Clarke, D.E., Gryspeerdt, J.L., Feyter, S.D., Voet, A.R.D.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders	Belgium	G0E4717N, G0F9316N, G051917N

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description