6P4O

Complex of XPB helicase with Bax1 endonuclease from Sulfurisphaera tokodaii at 3.15 Angstroms resolution

• PDB DOI: https://doi.org/10.2210/pdb6P4O/pdb

• Classification: HYDROLASE/DNA BINDING PROTEIN
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-28 Released: 2020-06-03 
• Deposition Author(s): Fan, L., DuPrez, K.T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.282 
• R-Value Work: 0.265 
• R-Value Observed: 0.266 

Literature

Complex of XPB helicase with Bax1 endonuclease from Sulfurisphaera tokodaii at 3.15 Angstroms resolution

Fan, L., DuPrez, K.T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 336.45 kDa 
• Atom Count: 20,038 
• Modelled Residue Count: 2,753 
• Deposited Residue Count: 2,880 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-dependent ATPase XPBII	A, C, E	459	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: xpb2, ST1613, STK_16130
UniProt
Find proteins for Q970I2 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970I2  Go to UniProtKB:  Q970I2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease Bax1	B, D, F	501	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: bax1, ST1614, STK_16140
UniProt
Find proteins for Q970I1 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970I1  Go to UniProtKB:  Q970I1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], L [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	H [auth A], I [auth A], J [auth A], M [auth F], N [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.282 
• R-Value Work: 0.265 
• R-Value Observed: 0.266 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.723	α = 90
b = 125.851	β = 101.52
c = 148.97	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
MOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Fan, L., DuPrez, K.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GMK8893

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description