3IJM | pdb_00003ijm

The structure of a restriction endonuclease-like fold superfamily protein from Spirosoma linguale.

• PDB DOI: https://doi.org/10.2210/pdb3IJM/pdb

• Classification: structural genomics, unknown function
• Organism(s): Spirosoma linguale DSM 74
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-08-04 Released: 2009-09-22 
• Deposition Author(s): Cuff, M.E., Tesar, C., Samano, S., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.199 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

The structure of a restriction endonuclease-like fold superfamily protein from Spirosoma linguale.

Cuff, M.E., Tesar, C., Samano, S., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.3 kDa 
• Atom Count: 2,669 
• Modeled Residue Count: 291 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized restriction endonuclease-like fold superfamily protein	A, B	151	Spirosoma linguale DSM 74	Mutation(s): 0  Gene Names: DUF820, SlinDRAFT_22400
UniProt
Find proteins for D2QNN3 (Spirosoma linguale (strain ATCC 33905 / DSM 74 / LMG 10896 / Claus 1)) Explore D2QNN3  Go to UniProtKB:  D2QNN3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	E [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: 1.70 Å
• R-Value Free:  0.199 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.77	α = 90
b = 65.849	β = 90
c = 68.917	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Cuff, M.E., Tesar, C., Samano, S., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary