6CMV | pdb_00006cmv

Crystal structure of Archaeal Biofilm Regulator (AbfR2) from Sulfolobus acidocaldarius

PDB DOI: https://doi.org/10.2210/pdb6CMV/pdb

Classification: GENE REGULATION
Organism(s): Sulfolobus acidocaldarius
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-03-06 Released: 2018-11-14
Deposition Author(s): Essen, L.-O., Vogt, M.S., Banerjee, A.
Funding Organization(s): Sonderforschungsbereich (SFB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.217 (Depositor), 0.221 (DCC)
R-Value Work:
0.166 (Depositor), 0.173 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of an Lrs14-like archaeal biofilm regulator from Sulfolobus acidocaldarius.

Vogt, M.S., Volpel, S.L., Albers, S.V., Essen, L.O., Banerjee, A.

(2018) Acta Crystallogr D Struct Biol 74: 1105-1114

PubMed: 30387769 Search on PubMed
DOI: https://doi.org/10.1107/S2059798318014146
Primary Citation Related Structures:
6CMV

PubMed Abstract:
The small winged helix-turn-helix (wHTH) proteins of the Lrs14 family are major transcriptional regulators and act as archaeal biofilm regulators (AbfRs) in the crenarchaeote Sulfolobus acidocaldarius. Here, the first crystal structure of an AbfR ortholog, AbfR2, the deletion of which is known to impair biofilm formation, is presented. Like most other wHTH orthologs, AbfR2 is dimeric in solution as well as in its 2.45 Å resolution crystal structure. Given the presence of three independent AbfR2 dimers in the asymmetric unit, the crystal structure shows a considerable degree of conformational variation within the dimer, the antiparallel orientations of which are stabilized by coiled-coil interaction between H4 helices. Conserved anchor interactions between helices H0 and H4 of AbfR2 further contribute to dimer stabilization. The combined structural and bioinformatic analysis reveals cluster-specific structural differences between different members of the Lrs14 protein family.

Organizational Affiliation

Structural Biochemistry - Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, 35032 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 101.16 kDa
Atom Count: 5,877
Modeled Residue Count: 670
Deposited Residue Count: 834
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator Lrs14-like protein	A, B, C, D, E A, B, C, D, E, F	139	Sulfolobus acidocaldarius	Mutation(s): 0 Gene Names: ATY89_00385, ATZ20_03430
UniProt
Find proteins for Q4J9G1 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore Q4J9G1 Go to UniProtKB: Q4J9G1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4J9G1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain X [auth F] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F]	J [auth A] K [auth A] L [auth A] M [auth B] Q [auth C] J [auth A], K [auth A], L [auth A], M [auth B], Q [auth C], R [auth D], S [auth D], T [auth D], U [auth E], W [auth F], X [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain V [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain V [auth F]	G [auth A] H [auth A] I [auth A] N [auth C] O [auth C] G [auth A], H [auth A], I [auth A], N [auth C], O [auth C], P [auth C], V [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain V [auth F]