3TXT | pdb_00003txt

Crystal structure of GlpG in complex with inhibitor DFP

• PDB DOI: https://doi.org/10.2210/pdb3TXT/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2011-09-23 Released: 2011-12-07 
• Deposition Author(s): Xue, Y., Ha, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.238 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

The crystal structure of rhomboid protease GlpG in complex with a mechanism-based inhibitor

Xue, Y., Ha, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.38 kDa 
• Atom Count: 1,422 
• Modeled Residue Count: 175 
• Deposited Residue Count: 179 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhomboid protease glpG	A	179	Escherichia coli K-12	Mutation(s): 0  Gene Names: glpG, b3424, JW5687 EC: 3.4.21.105 Membrane Entity: Yes
UniProt
Find proteins for P09391 (Escherichia coli (strain K12)) Explore P09391  Go to UniProtKB:  P09391

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DFP	B [auth A]	DIISOPROPYL PHOSPHONATE C6 H15 O3 P BLKXLEPPVDUHBY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.238 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.667	α = 90
b = 109.667	β = 90
c = 125.097	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Xue, Y., Ha, Y.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary