4EZG

Crystal structure of a putative cell adhesion protein (LMOf2365_1307) from Listeria monocytogenes str. 4b F2365 at 1.50 A resolution

PDB DOI: https://doi.org/10.2210/pdb4EZG/pdb

Classification: CELL ADHESION
Organism(s): Listeria monocytogenes ATCC 19115
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-05-02 Released: 2012-06-27
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.193
R-Value Work: 0.171
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of a leucine rich hypothetical protein (LMOf2365_1307) from Listeria monocytogenes str. Li 2 at 1.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 43.31 kDa
Atom Count: 3,574
Modelled Residue Count: 367
Deposited Residue Count: 394
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B	197	Listeria monocytogenes ATCC 19115	Mutation(s): 0 Gene Names: LMOf2365_1307
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.193
R-Value Work: 0.171
R-Value Observed: 0.172
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M34EZG

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.696	α = 90
b = 62.979	β = 90
c = 107.201	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
PHENIX	refinement
XDS	data reduction
SHELXD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-06-27

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2012-06-27
Type: Initial release
Version 1.1: 2012-07-11
Changes: Atomic model
Version 1.2: 2014-12-24
Changes: Structure summary
Version 1.3: 2017-11-15
Changes: Refinement description
Version 1.4: 2021-08-18
Changes: Database references, Derived calculations
Version 1.5: 2023-02-01
Changes: Database references
Version 1.6: 2024-11-20
Changes: Data collection, 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.