3IDF

The Crystal Structure of a USP-like protein from Wolinella succinogenes to 2.0A

• PDB DOI: https://doi.org/10.2210/pdb3IDF/pdb

• Classification: structural genomics, unknown function
• Organism(s): Wolinella succinogenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-07-21 Released: 2009-08-04 
• Deposition Author(s): Stein, A.J., Sather, A., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.217 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

The Crystal Structure of a USP-like protein from Wolinella succinogenes to 2.0A

Stein, A.J., Sather, A., Shackelford, G., 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)

Macromolecule Content

• Total Structure Weight: 31.53 kDa 
• Atom Count: 2,234 
• Modelled Residue Count: 273 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
USP-like protein	A, B	138	Wolinella succinogenes	Mutation(s): 0  Gene Names: ORF138, WS0834
UniProt
Find proteins for O34252 (Wolinella succinogenes) Explore O34252  Go to UniProtKB:  O34252

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.217 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.768	α = 90
b = 89.768	β = 90
c = 127.286	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: 2009-08-04 
Deposition Author(s): Stein, A.J., Sather, A., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations