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- PDB-6y45: Crystal Structure of the H33A variant of RsrR -

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Basic information

Entry
Database: PDB / ID: 6y45
TitleCrystal Structure of the H33A variant of RsrR
ComponentsRrf2 family transcriptional regulator
KeywordsTRANSCRIPTION / REDOX SENSOR / IRON SULFUR CLUSTER
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 / Rrf2 family transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsRohac, R. / Volbeda, 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.pdbx_dist_value / _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

Downloads & links

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Assembly

Deposited unit
A: Rrf2 family transcriptional regulator
B: Rrf2 family transcriptional regulator
C: Rrf2 family transcriptional regulator
D: Rrf2 family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,23919
Polymers69,2764
Non-polymers1,96315
Water7,927440
1
A: Rrf2 family transcriptional regulator
C: Rrf2 family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4628
Polymers34,6382
Non-polymers8246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-135 kcal/mol
Surface area15280 Å2
MethodPISA
2
B: Rrf2 family transcriptional regulator
D: Rrf2 family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,77611
Polymers34,6382
Non-polymers1,1399
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-162 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.920, 117.000, 71.330
Angle α, β, γ (deg.)90.000, 95.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Rrf2 family transcriptional regulator


Mass: 17318.904 Da / Num. of mol.: 4
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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: F2RGC9

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Non-polymers , 6 types, 455 molecules

#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: NaCl, MPD, MES, dithionite, anaerobic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.68→45.14 Å / Num. obs: 68787 / % possible obs: 96.5 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.062 / Net I/σ(I): 12.02
Reflection shellResolution: 1.68→1.78 Å / Rmerge(I) obs: 1.43 / Mean I/σ(I) obs: 0.67 / Num. unique obs: 10773 / CC1/2: 0.433 / Rrim(I) all: 1.66

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Processing

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

6hsd


Resolution: 1.68→45.14 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 6.836 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.1
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 3421 5 %RANDOM
Rwork0.1589 ---
obs0.1613 65117 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.56 Å2 / Biso mean: 37.062 Å2 / Biso min: 22.46 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20.67 Å2
2--0.29 Å20 Å2
3----1.95 Å2
Refinement stepCycle: final / Resolution: 1.68→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4562 0 91 440 5093
Biso mean--60.55 49.92 -
Num. residues----640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134846
X-RAY DIFFRACTIONr_bond_other_d0.0120.0174661
X-RAY DIFFRACTIONr_angle_refined_deg1.321.6476634
X-RAY DIFFRACTIONr_angle_other_deg1.5331.56910713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6695654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.81120.532188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34415690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9541536
X-RAY DIFFRACTIONr_chiral_restr0.0660.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025452
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02940
X-RAY DIFFRACTIONr_rigid_bond_restr2.4739507
LS refinement shellResolution: 1.68→1.724 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 246 -
Rwork0.38 4676 -
all-4922 -
obs--94.65 %

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