6P4F

Crystal structure of the XPB-Bax1-forked DNA ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of the XPB-Bax1-forked DNA ternary complex

He, F.Hilario, E.Fan, L.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-dependent ATPase XPBII
A, C
440Sulfurisphaera tokodaii str. 7Mutation(s): 0 
Gene Names: xpb2ST1613STK_16130
Find proteins for Q970I2 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Go to UniProtKB:  Q970I2
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Endonuclease Bax1
B, D
373Sulfurisphaera tokodaii str. 7Mutation(s): 0 
Gene Names: bax1ST1614STK_16140
Find proteins for Q970I1 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Go to UniProtKB:  Q970I1
Protein Feature View
  • Reference Sequence

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*AP*AP*CP*AP*TP*CP*CP*TP*TP*TP*GP*CP*TP*AP*CP*AP*A)-3')E, G24synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*TP*AP*GP*GP*TP*TP*TP*CP*CP*AP*TP*GP*TP*TP*GP*AP*GP*TP*CP*A)-3')F, H23synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
B, D, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B, D, G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D, E, F, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 214.687α = 90
b = 92.15β = 132.24
c = 172.128γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM108893

Revision History 

  • Version 1.0: 2020-06-17
    Type: Initial release