7PK5

Phosphodiesterase PdeL (EAL domain of crystals comprising full-length protein)

PDB DOI: https://doi.org/10.2210/pdb7PK5/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-08-25 Released: 2022-09-07
Deposition Author(s): Fadel, J., Schirmer, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.40 Å
R-Value Free: 0.397
R-Value Work: 0.373
R-Value Observed: 0.374

wwPDB Validation 3D Report Full Report

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

Literature

Phosphodiesterase PdeL (EAL domain of crystals comprising full-length protein)

Schirmer, T., Fadel, F.

To be published.

Macromolecule Content

Total Structure Weight: 166.68 kDa
Atom Count: 7,956
Modelled Residue Count: 1,012
Deposited Residue Count: 1,476
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic di-GMP phosphodiesterase PdeL	A, B [auth D], C [auth B], D [auth C]	369	Escherichia coli K-12	Mutation(s): 0 Gene Names: pdeL, yahA, b0315, JW0307 EC: 3.1.4.52
UniProt
Find proteins for P21514 (Escherichia coli (strain K12)) Explore P21514 Go to UniProtKB: P21514
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P21514
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.40 Å
R-Value Free: 0.397
R-Value Work: 0.373
R-Value Observed: 0.374
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.408	α = 90
b = 170.209	β = 94.37
c = 93.085	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-09-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-09-07
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, 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.