7BPU

Structural and mechanistic insights into the biosynthesis of Digeranylgeranylglyceryl phosphate synthase in membranes

PDB DOI: https://doi.org/10.2210/pdb7BPU/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli ATCC 8739
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2020-03-23 Released: 2021-04-14
Deposition Author(s): Cheng, W., Ren, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.32 Å
R-Value Free: 0.277
R-Value Work: 0.246
R-Value Observed: 0.247

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and Functional Insights into an Archaeal Lipid Synthase

Ren, S., de Kok, N.A., Gu, Y., Yan, W., Sun, Q., Chen, Y., He, J., Tian, L., Andringa, R.L., Zhu, X., Tang, M., Qi, S., Xu, H., Ren, H., Fu, X., Minnaard, A.J., Yang, S., Zhang, W., Li, W., Wei, Y., Driessen, A.J., Cheng, W.

(2020) Cell Rep 33: 108294

DOI: https://doi.org/10.1016/j.celrep.2020.108294

Macromolecule Content

Total Structure Weight: 63.76 kDa
Atom Count: 4,436
Modelled Residue Count: 558
Deposited Residue Count: 566
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Digeranylgeranylglyceryl phosphate synthase	A, B	283	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0 Gene Names: MJ0279 EC: 2.5.1.42 Membrane Entity: Yes
UniProt
Find proteins for Q57727 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57727 Go to UniProtKB: Q57727
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q57727
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.32 Å
R-Value Free: 0.277
R-Value Work: 0.246
R-Value Observed: 0.247
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.36	α = 90
b = 134.06	β = 90
c = 79.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data scaling
SHELXS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-04-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-04-14
Type: Initial release
Version 1.1: 2022-08-17
Changes: Database references, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.