3GS9 | pdb_00003gs9

Crystal structure of prophage tail protein gp18 (NP_465809.1) from Listeria monocytogenes EGD-e at 1.70 A resolution

PDB DOI: https://doi.org/10.2210/pdb3GS9/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Listeria monocytogenes EGD-e
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-26 Released: 2009-04-14
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of prophage tail protein gp18 (NP_465809.1) from Listeria monocytogenes EGD-e at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 40.43 kDa
Atom Count: 3,126
Modeled Residue Count: 326
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein gp18	A	342	Listeria monocytogenes EGD-e	Mutation(s): 0 Gene Names: lmo2285, NP_465809.1
UniProt
Find proteins for Q8Y4Z4 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y4Z4 Go to UniProtKB: Q8Y4Z4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8Y4Z4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET
OCS Query on OCS	A	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.223 (Depositor), 0.220 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33GS9

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.575	α = 90
b = 135.575	β = 90
c = 59.172	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-04-14

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-04-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references

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.