7PK5 | pdb_00007pk5

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 (Depositor), 0.402 (DCC)
R-Value Work:
0.373 (Depositor), 0.379 (DCC)
R-Value Observed:
0.374 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 1,012
Deposited Residue Count: 1,476
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.402 (DCC)
R-Value Work: 0.373 (Depositor), 0.379 (DCC)
R-Value Observed: 0.374 (Depositor)

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

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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

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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.