9JUE | pdb_00009jue

Roadblock3 homodimer structure from Candidatus Prometheoarchaeum syntrophicum strain MK-D1

PDB DOI: https://doi.org/10.2210/pdb9JUE/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Promethearchaeum syntrophicum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-10-08 Released: 2024-10-16
Deposition Author(s): Ponlachantra, K., Robinson, R.C.
Funding Organization(s): Vidyasirimedhi Institute of Science and Technology (VISTEC), Simons Foundation, Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.248 (Depositor), 0.248 (DCC)
R-Value Work:
0.209 (Depositor), 0.209 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Roadblock domain protein from Asgard archaea

Ponlachantra, K., Robinson, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 84.55 kDa
Atom Count: 5,571
Modeled Residue Count: 718
Deposited Residue Count: 786
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Roadblock/LC7 domain protein	A [auth D] B [auth C] C [auth B] D [auth A] E [auth F] A [auth D], B [auth C], C [auth B], D [auth A], E [auth F], F [auth E]	131	Promethearchaeum syntrophicum	Mutation(s): 0 Gene Names: DSAG12_02037
UniProt
Find proteins for A0A5B9DBI1 (Promethearchaeum syntrophicum) Explore A0A5B9DBI1 Go to UniProtKB: A0A5B9DBI1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5B9DBI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE (Subject of Investigation/LOI) Query on EPE Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.248 (Depositor), 0.248 (DCC)
R-Value Work: 0.209 (Depositor), 0.209 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.692	α = 90
b = 88.909	β = 90
c = 112.416	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-16

Deposition Author(s):

Ponlachantra, K.

Funding Organization	Location	Grant Number
Vidyasirimedhi Institute of Science and Technology (VISTEC)	Thailand	--
Simons Foundation	United States	GBMF9743
Other private	United States	Moore Foundation GBMF9743

Revision History (Full details and data files)

Version 1.0: 2024-10-16
Type: Initial release

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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.