6Y45 | pdb_00006y45

Crystal Structure of the H33A variant of RsrR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.205 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6Y45

This is version 1.2 of the entry. See complete history

Literature

Electron and Proton Transfers Modulate DNA Binding by the Transcription Regulator RsrR.

Crack, J.C.Amara, P.Volbeda, A.Mouesca, J.M.Rohac, R.Pellicer Martinez, M.T.Huang, C.Y.Gigarel, O.Rinaldi, C.Le Brun, N.E.Fontecilla-Camps, J.C.

(2020) J Am Chem Soc 142: 5104-5116

  • DOI: https://doi.org/10.1021/jacs.9b12250
  • Primary Citation Related Structures: 
    6Y42, 6Y45

  • PubMed Abstract: 

    The [Fe 2 S 2 ]-RsrR gene transcription regulator senses the redox status in bacteria by modulating DNA binding, while its cluster cycles between +1 and +2 states-only the latter binds DNA. We have previously shown that RsrR can undergo remarkable conformational changes involving a 100° rotation of tryptophan 9 between exposed ( Out ) and buried ( In ) states. Here, we have used the chemical modification of Trp9, site-directed mutagenesis, and crystallographic and computational chemical studies to show that (i) the Out and In states correspond to oxidized and reduced RsrR, respectively, (ii) His33 is protonated in the In state due to a change in its p K a caused by cluster reduction, and (iii) Trp9 rotation is conditioned by the response of its dipole moment to environmental electrostatic changes. Our findings illustrate a novel function of protonation resulting from electron transfer.


  • Organizational Affiliation
    • Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.

Macromolecule Content 

  • Total Structure Weight: 71.24 kDa 
  • Atom Count: 5,180 
  • Modeled Residue Count: 640 
  • Deposited Residue Count: 664 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rrf2 family transcriptional regulator
A, B, C, D
166Streptomyces venezuelae ATCC 10712Mutation(s): 1 
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2RGC9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES

Query on MES



Download:Ideal Coordinates CCD File
Q [auth D]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
FES
(Subject of Investigation/LOI)

Query on FES



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
O [auth C],
R [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
J [auth B]
M [auth B]
F [auth A],
G [auth A],
H [auth A],
J [auth B],
M [auth B],
N [auth B],
P [auth C],
S [auth D]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
K [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA

Query on NA



Download:Ideal Coordinates CCD File
L [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.205 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.92α = 90
b = 117β = 95.83
c = 71.33γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-18-CE11-0010
French National Research AgencyFranceANR-10-INSB-05-02

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description