7CQM | pdb_00007cqm

PlsY grown in LCP soaked with selenourea for 22 min

PDB DOI: https://doi.org/10.2210/pdb7CQM/pdb

Classification: TRANSFERASE
Organism(s): Aquifex aeolicus VF5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2020-08-11 Released: 2021-08-11
Deposition Author(s): Luo, Z.P., Li, D.F.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.190 (Depositor), 0.197 (DCC)
R-Value Work:
0.156 (Depositor), 0.170 (DCC)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7CQM

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Selenourea for experimental phasing of membrane protein crystals grown in lipid cubic phase

Luo, Z.P., Gu, W., Wang, Y., Tang, Y., Li, D.F.

(2022) Crystals (Basel) 12

DOI: https://doi.org/10.3390/cryst12070976

Macromolecule Content

Total Structure Weight: 52.64 kDa
Atom Count: 3,687
Modeled Residue Count: 400
Deposited Residue Count: 402
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol-3-phosphate acyltransferase	A, B	201	Aquifex aeolicus VF5	Mutation(s): 0 Gene Names: plsY, aq_676 EC: 2.3.1.275 Membrane Entity: Yes
UniProt
Find proteins for O66905 (Aquifex aeolicus (strain VF5)) Explore O66905 Go to UniProtKB: O66905
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O66905
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
79M Query on 79M Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain UA [auth B] SDF format, chain Z [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain TA [auth B] SDF format, chain T [auth A] SDF format, chain SA [auth B] SDF format, chain RA [auth B] SDF format, chain R [auth A] SDF format, chain QA [auth B] SDF format, chain Q [auth A] SDF format, chain PA [auth B] SDF format, chain P [auth A] SDF format, chain OA [auth B] SDF format, chain BA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain BA [auth B]	BA [auth B] OA [auth B] P [auth A] PA [auth B] Q [auth A] BA [auth B], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], W [auth A], X [auth A], Z [auth A]	(2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate C₁₉ H₃₆ O₄ OWGMAJRKMYGYBQ-HJCTWCACSA-N		Interactions Focus chain BA [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth A] Interactions & Density Focus chain BA [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth A]
SEY (Subject of Investigation/LOI) Query on SEY Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain C [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain Y [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth B] SDF format, chain G [auth A] 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 AA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] 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 AA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] 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]	AA [auth B] C [auth A] CA [auth B] D [auth A] DA [auth B] AA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], Y [auth A]	selenourea C H₄ N₂ Se IYKVLICPFCEZOF-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain C [auth A] 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 G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth B] Focus chain C [auth A] 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 G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain Y [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain O [auth A] SDF format, chain NA [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B]	IA [auth B] J [auth A] JA [auth B] K [auth A] KA [auth B] IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Interactions & Density Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.190 (Depositor), 0.197 (DCC)
R-Value Work: 0.156 (Depositor), 0.170 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.877	α = 90
b = 88.99	β = 95.19
c = 53.982	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2021-08-11
Type: Initial release
Version 1.1: 2022-08-31
Changes: Database references
Version 1.2: 2024-05-29
Changes: Data collection

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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.