3GCN | pdb_00003gcn

Crystal structure of DegS H198P/D320A mutant modified by DFP in complex with OMP peptide (YQF)

• PDB DOI: https://doi.org/10.2210/pdb3GCN/pdb

• Classification: HYDROLASE/HYDROLASE ACTIVATOR
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-02-22 Released: 2009-03-31 
• Deposition Author(s): Sohn, J., Sauer, R.T., Grant, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Mechanisms of allosteric activation of the DegS protease by OMP-peptide binding and protein-substrate binding

Sohn, J., Grant, R.A., Sauer, R.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)

Macromolecule Content 

• Total Structure Weight: 36.71 kDa 
• Atom Count: 2,251 
• Modeled Residue Count: 304 
• Deposited Residue Count: 343 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease degS	A	340	Escherichia coli K-12	Mutation(s): 2  Gene Names: b3235, degS, hhoB, htrH, JW3204 EC: 3.4.21 (PDB Primary Data), 3.4.21.107 (UniProt)
UniProt
Find proteins for P0AEE3 (Escherichia coli (strain K12)) Explore P0AEE3  Go to UniProtKB:  P0AEE3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
YQF peptide	B	3	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MIS	A	L-PEPTIDE LINKING	C6 H14 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.03	α = 90
b = 119.03	β = 90
c = 119.03	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-31 
Deposition Author(s): Sohn, J., Sauer, R.T., Grant, R.A.

Revision History  

• Version 1.0: 2009-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2012-12-12
  Changes: Other
• Version 1.3: 2013-03-13
  Changes: Other
• Version 1.4: 2017-11-01
  Changes: Refinement description
• Version 1.5: 2021-10-20
  Changes: Database references, Derived calculations