7B1L | pdb_00007b1l

Crystal structure of phosphatidyl serine synthase (PSS) in the closed conformation with bound citrate.

PDB DOI: https://doi.org/10.2210/pdb7B1L/pdb

Classification: LIPID BINDING PROTEIN
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2020-11-25 Released: 2021-12-08
Deposition Author(s): Yildiz, O., Centola, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.301 (Depositor), 0.300 (DCC)
R-Value Work:
0.263 (Depositor), 0.263 (DCC)
R-Value Observed:
0.265 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structures of phosphatidyl serine synthase PSS reveal the catalytic mechanism of CDP-DAG alcohol O-phosphatidyl transferases

Centola, M., Betz, H., Yildiz, O.

(2021) Nat Commun 12: 6982

DOI: https://doi.org/10.1038/s41467-021-27281-w

Macromolecule Content

Total Structure Weight: 55.57 kDa
Atom Count: 3,552
Modeled Residue Count: 400
Deposited Residue Count: 450
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CDP-diacylglycerol--serine O-phosphatidyltransferase	A, B	225	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0 Gene Names: pssA, MJ1212 EC: 2.7.8.8 Membrane Entity: Yes
UniProt
Find proteins for Q58609 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58609 Go to UniProtKB: Q58609
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58609
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
58A Query on 58A Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain C [auth A] MOL2 format, chain T [auth B] MOL2 format, chain C [auth A] mmCIF format, chain T [auth B] mmCIF format, chain C [auth A]	C [auth A], T [auth B]	5'-O-[(R)-{[(S)-{(2R)-2,3-bis[(9E)-octadec-9-enoyloxy]propoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine C₄₈ H₈₅ N₃ O₁₅ P₂ WVVFFOKRFKIBHD-ZIPNUMAKSA-N		Interactions Focus chain C [auth A] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain T [auth B]
OLC Query on OLC Download:Ideal Coordinates CCD File 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 BA [auth B] SDF format, chain AA [auth B] 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 BA [auth B] MOL2 format, chain AA [auth B] 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 BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] L [auth A] M [auth A] N [auth A] AA [auth B], BA [auth B], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] 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] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] 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]
SER Query on SER Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], X [auth B], Y [auth B]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain X [auth B] Focus chain Y [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain D [auth A] MOL2 format, chain U [auth B] MOL2 format, chain D [auth A] mmCIF format, chain U [auth B] mmCIF format, chain D [auth A]	D [auth A], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain U [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain S [auth B] SDF format, chain K [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain S [auth B] mmCIF format, chain K [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] K [auth A] S [auth B] V [auth B] E [auth A], F [auth A], K [auth A], S [auth B], V [auth B], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth A] Focus chain S [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth A] Focus chain S [auth B] Focus chain V [auth B] Focus chain W [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain J [auth A]	J [auth A], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain R [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain I [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain I [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain I [auth A]	I [auth A], Z [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain Z [auth B] Interactions & Density Focus chain I [auth A] Focus chain Z [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.301 (Depositor), 0.300 (DCC)
R-Value Work: 0.263 (Depositor), 0.263 (DCC)
R-Value Observed: 0.265 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.63	α = 90
b = 79.48	β = 90
c = 95.42	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-12-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-12-08
Type: Initial release
Version 1.1: 2024-10-09
Changes: Data collection, Structure summary

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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.