4GL0 | pdb_00004gl0

Putative spermidine/putrescine ABC transporter from Listeria monocytogenes

• PDB DOI: https://doi.org/10.2210/pdb4GL0/pdb

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


• Deposited: 2012-08-13 Released: 2012-08-22 
• Deposition Author(s): Osipiuk, J., Zhou, M., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.194 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

Putative spermidine/putrescine ABC transporter from Listeria monocytogenes

Osipiuk, J., Zhou, M., Papazisi, L., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.61 kDa 
• Atom Count: 2,931 
• Modeled Residue Count: 322 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lmo0810 protein	A	333	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: lmo0810
UniProt
Find proteins for Q8Y8T4 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y8T4  Go to UniProtKB:  Q8Y8T4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	C [auth A], D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	B [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.194 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34gl0

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.33	α = 90
b = 56.33	β = 90
c = 182.493	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-22 
Deposition Author(s): Osipiuk, J., Zhou, M., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-08-22
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary