4JZ5 | pdb_00004jz5

High-resolution structure of catalytic domain of endolysin ply40 from bacteriophage P40 of Listeria monocytogenes

PDB DOI: https://doi.org/10.2210/pdb4JZ5/pdb

Classification: HYDROLASE
Organism(s): Listeria phage P40
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-04-02 Released: 2014-04-09
Deposition Author(s): Romero-Fernandez, P., Bartual, S.G., Carrasco-lopez, C., Hermoso, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.143 (Depositor), 0.144 (DCC)
R-Value Work:
0.134 (Depositor), 0.135 (DCC)
R-Value Observed:
0.135 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of catalytic domain of endolysin Ply40

Romero-Fernandez, P., Bartual, S.G., Carrasco-lopez, C., Loessner, M., Hermoso, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 25.08 kDa
Atom Count: 2,016
Modeled Residue Count: 206
Deposited Residue Count: 223
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gp26	A	223	Listeria phage P40	Mutation(s): 0 Gene Names: gp26
UniProt
Find proteins for A0ACD6B8G2 (Listeria phage P40) Explore A0ACD6B8G2 Go to UniProtKB: A0ACD6B8G2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8G2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.143 (Depositor), 0.144 (DCC)
R-Value Work: 0.134 (Depositor), 0.135 (DCC)
R-Value Observed: 0.135 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.332	α = 90
b = 42.332	β = 90
c = 98.627	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-04-09

Deposition Author(s):

Romero-Fernandez, P.

Carrasco-lopez, C.

Revision History (Full details and data files)

Version 1.0: 2014-04-09
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, 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.