6S3Y | pdb_00006s3y

CBDP35 SeMet structure

PDB DOI: https://doi.org/10.2210/pdb6S3Y/pdb

Classification: HYDROLASE
Organism(s): Listeria phage P35
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2019-06-26 Released: 2020-07-15
Deposition Author(s): Hermoso, J.A., Bartual, S.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.226 (Depositor), 0.230 (DCC)
R-Value Work:
0.203 (Depositor), 0.210 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

CBDP35 SeMet structure

Hermoso, J.A., Bartual, S.G.

To be published.

Macromolecule Content

Total Structure Weight: 196.99 kDa
Atom Count: 15,137
Modeled Residue Count: 1,665
Deposited Residue Count: 1,680
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PlyP35	A B C D E A, B, C, D, E, F, G, H, I, J, K [auth L], L [auth K]	140	Listeria phage P35	Mutation(s): 0 Gene Names: ply
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A B C D E A, B, C, D, E, F, G, H, I, J, K [auth L], L [auth K]	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.226 (Depositor), 0.230 (DCC)
R-Value Work: 0.203 (Depositor), 0.210 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 335.878	α = 90
b = 95.565	β = 90
c = 84.408	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-07-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-07-15
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Refinement description, Structure summary

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.