9J8Q | pdb_00009j8q

MprF from Pseudomonas aeruginosa in GDN micelle, C2 symmetry

PDB DOI: https://doi.org/10.2210/pdb9J8Q/pdb
EM Map EMD-61238: EMDB EMDataResource

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

Deposited: 2024-08-21 Released: 2025-09-03
Deposition Author(s): Jha, S., Vinothkumar, K.R.
Funding Organization(s): Other government, Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9J8Q

This is version 1.0 of the entry. See complete history.

Literature

Structures of Multiple Peptide Resistance Factor from Pseudomonas aeruginosa

Jha, S., Vinothkumar, K.R.

To be published.

Macromolecule Content

Total Structure Weight: 224.32 kDa
Atom Count: 13,056
Modeled Residue Count: 1,598
Deposited Residue Count: 1,806
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylglycerol lysyltransferase	A, B	903	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: PA0920 EC: 2.3.2.3 Membrane Entity: Yes
UniProt
Find proteins for Q9I537 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I537 Go to UniProtKB: Q9I537
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I537
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J4U Query on J4U Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain C [auth A] MOL2 format, chain W [auth B] MOL2 format, chain C [auth A] mmCIF format, chain W [auth B] mmCIF format, chain C [auth A]	C [auth A], W [auth B]	(2~{R},3~{S},4~{S},5~{S},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{S},4~{R},5~{R},6~{R})-2-(hydroxymethyl)-6-[2-[[(2~{R},3~{S},4~{R},5~{R},6~{S})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]oxymethyl]-4-[(1~{R},2~{R},4~{S},5'~{R},6~{R},7~{R},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxy-butoxy]-4,5-bis(oxidanyl)oxan-3-yl]oxy-oxane-3,4,5-triol C₅₆ H₉₂ O₂₅ LKBFXDNKNZXHHW-RFRGGUJUSA-N		Interactions Focus chain C [auth A] Focus chain W [auth B] Interactions & Density Focus chain C [auth A] Focus chain W [auth B]
PGT Query on PGT Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth A] SDF format, chain S [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 HA [auth B] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth B] SDF format, chain D [auth A] SDF format, chain CA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [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 HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth A] mmCIF format, chain S [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 HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain CA [auth B]	CA [auth B] D [auth A] DA [auth B] E [auth A] EA [auth B] CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], GA [auth B], HA [auth B], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], S [auth A], T [auth A], U [auth B], V [auth B], X [auth B], Y [auth B], Z [auth B]	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C₄₀ H₇₉ O₁₀ P KBPVYRBBONZJHF-AMAPPZPBSA-N		Interactions Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] 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 S [auth A] Focus chain T [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] 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 S [auth A] Focus chain T [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
PTY Query on PTY Download:Ideal Coordinates CCD File 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 LA [auth B] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain BA [auth B] SDF format, chain AA [auth B] 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 LA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] 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 LA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] G [auth A] H [auth A] IA [auth B] AA [auth B], BA [auth B], G [auth A], H [auth A], IA [auth B], JA [auth B], KA [auth B], LA [auth B], O [auth A], P [auth A], Q [auth A], R [auth A]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1-4487
MODEL REFINEMENT	REFMAC	5.8.0411
RECONSTRUCTION	cryoSPARC	4.3

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Vinothkumar, K.R.

Funding Organization	Location	Grant Number
Other government		Department of Atomic Energy, Government of India, RTI 4006
Department of Biotechnology (DBT, India)	India	DBT/PR12422/MED/31/287/2014

Revision History (Full details and data files)

Version 1.0: 2025-09-03
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.