3TXT

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.238
R-Value Work: 0.219
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

Xue, Y., Ha, Y.

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09391
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DFP Query on DFP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	DIISOPROPYL PHOSPHONATE C₆ H₁₅ O₃ P BLKXLEPPVDUHBY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.238
R-Value Work: 0.219
R-Value Observed: 0.220
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-12-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-12-07
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description

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 R01GM133198.