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), 0.223 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3GS9

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.223 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data:

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

View more in-depth experimental data

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

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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.