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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.249 (Depositor), 0.247 (DCC)
R-Value Work:
0.213 (Depositor), 0.210 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history.

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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AEE3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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 Query on 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), 0.247 (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

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Entry History

Deposition Data

Released Date: 2009-03-31

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.