3IUO

The Crystal Structure of the C-terminal domain of the ATP-dependent DNA helicase RecQ from Porphyromonas gingivalis to 1.6A

• PDB DOI: https://doi.org/10.2210/pdb3IUO/pdb

• Classification: HYDROLASE
• Organism(s): Porphyromonas gingivalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-31 Released: 2009-09-08 
• Deposition Author(s): Stein, A.J., Sather, A., Duggan, E., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.221 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

The Crystal Structure of the C-terminal domain of the ATP-dependent DNA helicase RecQ from Porphyromonas gingivalis to 1.6A

Stein, A.J., Sather, A., Duggan, E., Moy, S., Joachimiak, 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)

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.12 kDa 
• Atom Count: 1,999 
• Modelled Residue Count: 221 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA helicase RecQ	A, B	122	Porphyromonas gingivalis	Mutation(s): 0  Gene Names: PG0684, PG_0416, recQ-1
UniProt
Find proteins for Q7MX11 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MX11  Go to UniProtKB:  Q7MX11

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.221 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.326	α = 90
b = 98.326	β = 90
c = 72.526	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Stein, A.J., Sather, A., Duggan, E., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description