6YJ1 | pdb_00006yj1

The M23 peptidase domain of the Staphylococcal phage 2638A endolysin

PDB DOI: https://doi.org/10.2210/pdb6YJ1/pdb

Classification: VIRAL PROTEIN
Organism(s): Staphylococcus phage 2638A
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-04-02 Released: 2020-09-09
Deposition Author(s): Dunne, M., Ernst, P., Sobieraj, A., Pluckthun, A., Loessner, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.310 (Depositor), 0.310 (DCC)
R-Value Work:
0.251 (Depositor), 0.252 (DCC)
R-Value Observed:
0.254 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

(CASP target) Crystal structure of the M23 peptidase domain of Staphylococcal phage 2638A endolysin

Sobieraj, A., Dunne, M., Ernst, P., Pluckthun, A., Loessner, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 42.7 kDa
Atom Count: 2,826
Modeled Residue Count: 338
Deposited Residue Count: 372
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORF007	A, B	186	Staphylococcus phage 2638A	Mutation(s): 0 EC: 3.5.1.28
UniProt
Find proteins for Q4ZD58 (Staphylococcus phage 2638A) Explore Q4ZD58 Go to UniProtKB: Q4ZD58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4ZD58
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.310 (Depositor), 0.310 (DCC)
R-Value Work: 0.251 (Depositor), 0.252 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.89	α = 90
b = 56.38	β = 92.84
c = 110.49	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-09-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-09-09
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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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.