6M31 | pdb_00006m31

Structural and Functional Insights into an Archaeal Lipid Synthase

PDB DOI: https://doi.org/10.2210/pdb6M31/pdb

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

Deposited: 2020-03-02 Released: 2021-02-03
Deposition Author(s): Ren, S., Cheng, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.230 (Depositor), 0.240 (DCC)
R-Value Work:
0.201 (Depositor), 0.208 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6M31

Ligand Structure Quality Assessment

This is version 1.3 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: 75.79 kDa
Atom Count: 5,336
Modeled Residue Count: 560
Deposited Residue Count: 566
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q57727
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPG (Subject of Investigation/LOI) Query on MPG Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] R [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], R [auth A], S [auth A], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], Z [auth A]	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate C₂₁ H₄₀ O₄ JPJYKWFFJCWMPK-GDCKJWNLSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain R [auth A] Focus chain S [auth A] 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 VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain R [auth A] Focus chain S [auth A] 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 VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain Z [auth A]
LDA (Subject of Investigation/LOI) Query on LDA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B]	C [auth A] D [auth A] E [auth A] EA [auth B] F [auth A] C [auth A], D [auth A], 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], 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], NA [auth B], OA [auth B], PA [auth B]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] 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 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 NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] 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 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 NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth B] SDF format, chain RA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B]	N [auth A], O [auth A], P [auth A], QA [auth B], RA [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth B] Focus chain RA [auth B] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth B] Focus chain RA [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain SA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain SA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain SA [auth B]	Q [auth A], SA [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain SA [auth B] Interactions & Density Focus chain Q [auth A] Focus chain SA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.230 (Depositor), 0.240 (DCC)
R-Value Work: 0.201 (Depositor), 0.208 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70	α = 90
b = 133.49	β = 90
c = 79.5	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-02-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-02-03
Type: Initial release
Version 1.1: 2021-08-18
Changes: Database references, Structure summary
Version 1.2: 2022-08-17
Changes: Database references, Structure summary
Version 1.3: 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.