4HN3 | pdb_00004hn3

The crystal structure of a sex pheromone precursor (lmo1757) from Listeria monocytogenes EGD-e

PDB DOI: https://doi.org/10.2210/pdb4HN3/pdb

Classification: SIGNALING PROTEIN
Organism(s): Listeria monocytogenes EGD-e
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-10-18 Released: 2012-10-31
Deposition Author(s): Tan, K., Makowska-Grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.221 (Depositor), 0.216 (DCC)
R-Value Work:
0.181 (Depositor), 0.178 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of a sex pheromone precursor (lmo1757) from Listeria monocytogenes EGD-e

Tan, K., Makowska-Grzyska, M., Kwon, K., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 159.6 kDa
Atom Count: 11,113
Modeled Residue Count: 1,324
Deposited Residue Count: 1,400
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo1757 protein	A, B, C, D	350	Listeria monocytogenes EGD-e	Mutation(s): 0 Gene Names: lmo1757
UniProt
Find proteins for Q8Y6D1 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y6D1 Go to UniProtKB: Q8Y6D1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8Y6D1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] G [auth A] H [auth A] I [auth A] P [auth B] AA [auth D], G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], V [auth C], Y [auth D], Z [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	E [auth A] F [auth A] K [auth B] L [auth B] M [auth B] E [auth A], F [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C], U [auth C], W [auth D], X [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.221 (Depositor), 0.216 (DCC)
R-Value Work: 0.181 (Depositor), 0.178 (DCC)
R-Value Observed: 0.183 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34hn3

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.085	α = 90
b = 99.318	β = 90
c = 104.608	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-10-31

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-10-31
Type: Initial release
Version 1.1: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary