6HSM | pdb_00006hsm

Structure of partially reduced RsrR in space group P2(1)2(1)2(1)

PDB DOI: https://doi.org/10.2210/pdb6HSM/pdb

Classification: TRANSCRIPTION
Organism(s): Streptomyces venezuelae ATCC 10712
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-10-01 Released: 2019-01-30
Deposition Author(s): Volbeda, A., Fontecilla-Camps, J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.230 (Depositor), 0.236 (DCC)
R-Value Work:
0.195 (Depositor), 0.203 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Transcription Regulator RsrR Reveals a [2Fe-2S] Cluster Coordinated by Cys, Glu, and His Residues.

Volbeda, A., Martinez, M.T.P., Crack, J.C., Amara, P., Gigarel, O., Munnoch, J.T., Hutchings, M.I., Darnault, C., Le Brun, N.E., Fontecilla-Camps, J.C.

(2019) J Am Chem Soc 141: 2367-2375

PubMed: 30657661 Search on PubMed
DOI: https://doi.org/10.1021/jacs.8b10823
Primary Citation Related Structures:
6HSD, 6HSE, 6HSM

PubMed Abstract:
The recently discovered Rrf2 family transcriptional regulator RsrR coordinates a [2Fe-2S] cluster. Remarkably, binding of the protein to RsrR-regulated promoter DNA sequences is switched on and off through the facile cycling of the [2Fe-2S] cluster between +2 and +1 states. Here, we report high resolution crystal structures of the RsrR dimer, revealing that the [2Fe-2S] cluster is asymmetrically coordinated across the RsrR monomer-monomer interface by two Cys residues from one subunit and His and Glu residues from the other. To our knowledge, this is the first example of a protein bound [Fe-S] cluster with three different amino acid side chains as ligands, and of Glu acting as ligand to a [2Fe-2S] cluster. Analyses of RsrR structures revealed a conformational change, centered on Trp9, which results in a significant shift in the DNA-binding helix-turn-helix region.

Organizational Affiliation

Université Grenoble Alpes, CEA, CNRS , IBS , Metalloproteins Unit, F-38044 Grenoble , France.

Macromolecule Content

Total Structure Weight: 144.59 kDa
Atom Count: 10,355
Modeled Residue Count: 1,276
Deposited Residue Count: 1,328
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rrf2 family transcriptional regulator	A B [auth D] C [auth B] D [auth C] E A, B [auth D], C [auth B], D [auth C], E, F [auth G], G [auth F], H	166	Streptomyces venezuelae ATCC 10712	Mutation(s): 0 Gene Names: SVEN_6563
UniProt
Find proteins for F2RGC9 (Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745)) Explore F2RGC9 Go to UniProtKB: F2RGC9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F2RGC9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain QA [auth E] MOL2 format, chain QA [auth E] mmCIF format, chain QA [auth E]	QA [auth E]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain QA [auth E] Interactions & Density Focus chain QA [auth E]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain ZA [auth F] SDF format, chain Z [auth B] SDF format, chain UA [auth F] SDF format, chain Q [auth A] SDF format, chain NA [auth E] SDF format, chain MA [auth E] SDF format, chain IA [auth B] SDF format, chain I [auth A] MOL2 format, chain ZA [auth F] MOL2 format, chain Z [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain Q [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] mmCIF format, chain ZA [auth F] mmCIF format, chain Z [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain Q [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain MA [auth E] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A]	I [auth A] IA [auth B] MA [auth E] NA [auth E] Q [auth A] I [auth A], IA [auth B], MA [auth E], NA [auth E], Q [auth A], UA [auth F], Z [auth B], ZA [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain IA [auth B] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain Q [auth A] Focus chain UA [auth F] Focus chain Z [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain I [auth A] Focus chain IA [auth B] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain Q [auth A] Focus chain UA [auth F] Focus chain Z [auth B] Focus chain ZA [auth F]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain WA [auth F] SDF format, chain W [auth D] SDF format, chain VA [auth F] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain TA [auth G] SDF format, chain T [auth D] SDF format, chain SA [auth G] SDF format, chain S [auth D] SDF format, chain RA [auth G] SDF format, chain R [auth D] SDF format, chain OA [auth E] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BB [auth H] SDF format, chain BA [auth B] SDF format, chain AB [auth H] SDF format, chain AA [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain W [auth D] MOL2 format, chain VA [auth F] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain TA [auth G] MOL2 format, chain T [auth D] MOL2 format, chain SA [auth G] MOL2 format, chain S [auth D] MOL2 format, chain RA [auth G] MOL2 format, chain R [auth D] MOL2 format, chain OA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BB [auth H] MOL2 format, chain BA [auth B] MOL2 format, chain AB [auth H] MOL2 format, chain AA [auth B] mmCIF format, chain WA [auth F] mmCIF format, chain W [auth D] mmCIF format, chain VA [auth F] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain TA [auth G] mmCIF format, chain T [auth D] mmCIF format, chain SA [auth G] mmCIF format, chain S [auth D] mmCIF format, chain RA [auth G] mmCIF format, chain R [auth D] mmCIF format, chain OA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BB [auth H] mmCIF format, chain BA [auth B] mmCIF format, chain AB [auth H] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth H] BA [auth B] BB [auth H] CA [auth B] AA [auth B], AB [auth H], BA [auth B], BB [auth H], CA [auth B], DA [auth B], EA [auth B], FA [auth B], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], M [auth A], N [auth A], O [auth A], OA [auth E], R [auth D], RA [auth G], S [auth D], SA [auth G], T [auth D], TA [auth G], U [auth D], V [auth D], VA [auth F], W [auth D], WA [auth F]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain AA [auth B] Focus chain AB [auth H] Focus chain BA [auth B] Focus chain BB [auth H] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth E] Focus chain R [auth D] Focus chain RA [auth G] Focus chain S [auth D] Focus chain SA [auth G] Focus chain T [auth D] Focus chain TA [auth G] Focus chain U [auth D] Focus chain V [auth D] Focus chain VA [auth F] Focus chain W [auth D] Focus chain WA [auth F] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth H] Focus chain BA [auth B] Focus chain BB [auth H] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth E] Focus chain R [auth D] Focus chain RA [auth G] Focus chain S [auth D] Focus chain SA [auth G] Focus chain T [auth D] Focus chain TA [auth G] Focus chain U [auth D] Focus chain V [auth D] Focus chain VA [auth F] Focus chain W [auth D] Focus chain WA [auth F]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain XA [auth F] SDF format, chain X [auth D] SDF format, chain PA [auth E] SDF format, chain P [auth A] SDF format, chain LA [auth C] MOL2 format, chain XA [auth F] MOL2 format, chain X [auth D] MOL2 format, chain PA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain LA [auth C] mmCIF format, chain XA [auth F] mmCIF format, chain X [auth D] mmCIF format, chain PA [auth E] mmCIF format, chain P [auth A] mmCIF format, chain LA [auth C]	LA [auth C], P [auth A], PA [auth E], X [auth D], XA [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain LA [auth C] Focus chain P [auth A] Focus chain PA [auth E] Focus chain X [auth D] Focus chain XA [auth F] Interactions & Density Focus chain LA [auth C] Focus chain P [auth A] Focus chain PA [auth E] Focus chain X [auth D] Focus chain XA [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain YA [auth F] SDF format, chain Y [auth D] SDF format, chain GA [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain Y [auth D] MOL2 format, chain GA [auth B] mmCIF format, chain YA [auth F] mmCIF format, chain Y [auth D] mmCIF format, chain GA [auth B]	GA [auth B], Y [auth D], YA [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain GA [auth B] Focus chain Y [auth D] Focus chain YA [auth F] Interactions & Density Focus chain GA [auth B] Focus chain Y [auth D] Focus chain YA [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain HA [auth B]	HA [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Interactions & Density Focus chain HA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.230 (Depositor), 0.236 (DCC)
R-Value Work: 0.195 (Depositor), 0.203 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.65	α = 90
b = 129.84	β = 90
c = 170.3	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Volbeda, A.

Fontecilla-Camps, J.C.

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release
Version 1.1: 2019-02-13
Changes: Data collection, Database references
Version 1.2: 2019-02-20
Changes: Data collection, Database references
Version 1.3: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description