7B1N | pdb_00007b1n

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

• PDB DOI: https://doi.org/10.2210/pdb7B1N/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.355 (Depositor), 0.350 (DCC) 
• R-Value Work: 
  0.302 (Depositor), 0.300 (DCC) 
• R-Value Observed: 
  0.305 (Depositor) 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.66 kDa 
• Atom Count: 3,226 
• Modeled Residue Count: 400 
• Deposited Residue Count: 450 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
58A	C [auth A], G [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
CA	D [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A], F [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.355 (Depositor), 0.350 (DCC) 
• R-Value Work:  0.302 (Depositor), 0.300 (DCC) 
• R-Value Observed: 0.305 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.13	α = 90
b = 70.81	β = 90
c = 94.09	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-08 
Deposition Author(s): Yildiz, O., Centola, M.

Revision History  

• Version 1.0: 2021-12-08
  Type: Initial release
  
• Version 2.0: 2022-10-26
  Changes: Advisory, Database references, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2024-11-06
  Changes: Data collection, Structure summary