8Q2O | pdb_00008q2o

Structure of alginate transporter AlgE from P. aeruginosa PAO1 by using Se-MAG for the the lipid cubic phase crystallization

PDB DOI: https://doi.org/10.2210/pdb8Q2O/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-08-03 Released: 2024-05-15
Deposition Author(s): Huang, C.-Y., Boland, C., Kaki, S.S., Wang, M., Olieric, V., Caffrey, M.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission, Science Foundation Ireland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.199 (Depositor), 0.202 (DCC)
R-Value Work:
0.163 (Depositor), 0.167 (DCC)
R-Value Observed:
0.165 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Se-MAG Is a Convenient Additive for Experimental Phasing and Structure Determination of Membrane Proteins Crystallised by the Lipid Cubic Phase (In Meso) Method

Boland, C., Huang, C.Y., Shanker Kaki, S., Wang, M., Olieric, V., Caffrey, M.

(2023) Crystals (Basel)

DOI: https://doi.org/10.3390/cryst13091402

Macromolecule Content

Total Structure Weight: 61.41 kDa
Atom Count: 4,525
Modeled Residue Count: 460
Deposited Residue Count: 479
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alginate production protein AlgE	A	479	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: algE, alg76, PA3544 Membrane Entity: Yes
UniProt
Find proteins for P18895 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P18895 Go to UniProtKB: P18895
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18895
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE5 Query on PE5 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C₁₈ H₃₈ O₉ CUDPPTPIUWYGFI-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
IRY (Subject of Investigation/LOI) Query on IRY Download:Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain W [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain W [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], W [auth A]	[(2~{S})-2,3-bis(oxidanyl)propyl] 8-hexylselanyloctanoate C₁₇ H₃₄ O₄ Se NDMGORYXSUYATF-INIZCTEOSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth A]
C8E Query on C8E Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain V [auth A] MOL2 format, chain X [auth A] MOL2 format, chain V [auth A] mmCIF format, chain X [auth A] mmCIF format, chain V [auth A]	V [auth A], X [auth A]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N		Interactions Focus chain V [auth A] Focus chain X [auth A] Interactions & Density Focus chain V [auth A] Focus chain X [auth A]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain Y [auth A]	Y [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain Y [auth A] Interactions & Density Focus chain Y [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A], BA [auth A], C [auth A], D [auth A], Z [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.199 (Depositor), 0.202 (DCC)
R-Value Work: 0.163 (Depositor), 0.167 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.09	α = 90
b = 74.49	β = 102.5
c = 115.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELXCD	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-15

Deposition Author(s):

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	701647
Science Foundation Ireland	Ireland	16/IA/4435

Revision History (Full details and data files)

Version 1.0: 2024-05-15
Type: Initial release

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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.