7A66 | pdb_00007a66

structure of Pcc2 from Pyrococcus abyssi

• PDB DOI: https://doi.org/10.2210/pdb7A66/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Pyrococcus abyssi GE5
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2020-08-25 Released: 2022-03-23 
• Deposition Author(s): Missoury, S., Tilbeurgh, V.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Structure of Pcc2 at 1.84 Angstroms resolution

Missoury, S., Tilbeurgh, V.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.84 kDa 
• Atom Count: 2,091 
• Modeled Residue Count: 255 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pcc2	A, B, C	86	Pyrococcus abyssi GE5	Mutation(s): 0
UniProt
Find proteins for A0A915Q983 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore A0A915Q983  Go to UniProtKB:  A0A915Q983

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth B], G [auth C], H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B, C	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.8	α = 90
b = 81.31	β = 121.59
c = 66.48	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-03-23 
Deposition Author(s): Missoury, S., Tilbeurgh, V.H.

Revision History  

• Version 1.0: 2022-03-23
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary