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- PDB-6y42: Crystal Structure of RsrR complexed to a 39 basepair DNA fragment... -

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Basic information

Entry
Database: PDB / ID: 6y42
TitleCrystal Structure of RsrR complexed to a 39 basepair DNA fragment of the rsrR promoter
Components
  • (DNA (39-MER)) x 2
  • Rrf2 family transcriptional regulator
KeywordsTRANSCRIPTION / REDOX SENSOR / IRON SULFUR CLUSTER / DNA COMPLEX
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / DNA-binding transcription factor activity / metal ion binding / cytosol
Similarity search - Function
Transcription regulator Rrf2-type, conserved site / Rrf2-type HTH domain signature. / Transcription regulator Rrf2 / Iron-dependent Transcriptional regulator / Rrf2-type HTH domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / DNA / DNA (> 10) / Rrf2 family transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
Streptomyces venezuelae ATCC 10712 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.3 Å
AuthorsVolbeda, A. / Fontecilla-Camps, J.C.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE11-0010 France
French National Research AgencyANR-10-INSB-05-02 France
Citation
Journal: J.Am.Chem.Soc. / Year: 2020
Title: Electron and Proton Transfers Modulate DNA Binding by the Transcription Regulator RsrR.
Authors: 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.
#1: Journal: J. Am. Chem. Soc. / Year: 2019
Title: Crystal Structure of the Transcription Regulator RsrR Reveals a [2Fe-2S] Cluster Coordinated by Cys, Glu, and His Residues.
Authors: 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.
History
DepositionFeb 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rrf2 family transcriptional regulator
B: Rrf2 family transcriptional regulator
E: DNA (39-MER)
F: DNA (39-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1306
Polymers58,7784
Non-polymers3522
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12620 Å2
ΔGint-120 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.370, 197.370, 73.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Rrf2 family transcriptional regulator


Mass: 17385.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (bacteria)
Gene: SVEN_6563 / Plasmid: pGS-21a / Cell line (production host): BL21(DE3)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F2RGC9
#2: DNA chain DNA (39-MER)


Mass: 12127.805 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Streptomyces venezuelae ATCC 10712 (bacteria)
#3: DNA chain DNA (39-MER)


Mass: 11878.648 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Streptomyces venezuelae ATCC 10712 (bacteria)
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: NaCl, MgCl2, CaCl2, PEG1000, PEG3350, MES, anaerobic (in glove box)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 4.3→49.34 Å / Num. obs: 6038 / % possible obs: 99.5 % / Redundancy: 5.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.057 / Rrim(I) all: 0.104 / Net I/σ(I): 8.8
Reflection shellResolution: 4.3→4.45 Å / Rmerge(I) obs: 2.13 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3563 / CC1/2: 0.36 / Rpim(I) all: 0.988 / Rrim(I) all: 2.53

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6hsd

6hsd


Resolution: 4.3→49.34 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.939 / SU B: 132.744 / SU ML: 1.358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.077
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3002 330 5.5 %RANDOM
Rwork0.2668 ---
obs0.2684 5671 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 387.16 Å2 / Biso mean: 253.122 Å2 / Biso min: 185.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å21.08 Å20 Å2
2--2.17 Å20 Å2
3----7.03 Å2
Refinement stepCycle: final / Resolution: 4.3→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 1476 8 0 3766
Biso mean--237.54 --
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124179
X-RAY DIFFRACTIONr_bond_other_d0.0020.0183080
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.4385740
X-RAY DIFFRACTIONr_angle_other_deg1.3061.9577162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4335316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.83220.56289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41815348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0981517
X-RAY DIFFRACTIONr_chiral_restr0.0490.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023482
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02797
LS refinement shellResolution: 4.3→4.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.499 28 -
Rwork0.454 386 -
all-414 -
obs--97.64 %

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