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- PDB-7kfq: Crystal structure of the MarR family transcriptional regulator fr... -

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Basic information

Entry
Database: PDB / ID: 7kfq
TitleCrystal structure of the MarR family transcriptional regulator from Variovorax paradoxus bound to 1H-Indole-3-Carboxylic Acid
ComponentsTranscriptional regulator, MarR family
KeywordsDNA BINDING PROTEIN / Transcriptional Regulator / Ligand Binding
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
: / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
1H-INDOLE-3-CARBOXYLIC ACID / Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsWalton, W.G. / Redinbo, M.R. / Dangl, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS-1917270 United States
CitationJournal: Nat Microbiol / Year: 2022
Title: Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome.
Authors: Conway, J.M. / Walton, W.G. / Salas-Gonzalez, I. / Law, T.F. / Lindberg, C.A. / Crook, L.E. / Kosina, S.M. / Fitzpatrick, C.R. / Lietzan, A.D. / Northen, T.R. / Jones, C.D. / Finkel, O.M. / ...Authors: Conway, J.M. / Walton, W.G. / Salas-Gonzalez, I. / Law, T.F. / Lindberg, C.A. / Crook, L.E. / Kosina, S.M. / Fitzpatrick, C.R. / Lietzan, A.D. / Northen, T.R. / Jones, C.D. / Finkel, O.M. / Redinbo, M.R. / Dangl, J.L.
History
DepositionOct 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2273
Polymers20,9701
Non-polymers2572
Water2,324129
1
A: Transcriptional regulator, MarR family
hetero molecules

A: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4546
Polymers41,9392
Non-polymers5144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.683, 114.277, 114.907
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-369-

HOH

21A-404-

HOH

31A-428-

HOH

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Components

#1: Protein Transcriptional regulator, MarR family


Mass: 20969.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: Vapar_1489 / Production host: Escherichia coli (E. coli) / References: UniProt: C5CSP2
#2: Chemical ChemComp-ICO / 1H-INDOLE-3-CARBOXYLIC ACID


Mass: 161.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium Sulfate, 0.1 M Tris: HCl, pH 8.5, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.35→45.33 Å / Num. obs: 39480 / % possible obs: 99.69 % / Redundancy: 2 % / Biso Wilson estimate: 19.61 Å2 / CC1/2: 1 / Net I/σ(I): 20.95
Reflection shellResolution: 1.35→1.398 Å / Num. unique obs: 3842 / CC1/2: 0.763

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KFO

7kfo


Resolution: 1.35→45.33 Å / SU ML: 0.1063 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1524
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2222 1999 5.06 %
Rwork0.1867 37480 -
obs0.1885 39479 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.7 Å2
Refinement stepCycle: LAST / Resolution: 1.35→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 17 129 1291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651324
X-RAY DIFFRACTIONf_angle_d0.89251809
X-RAY DIFFRACTIONf_chiral_restr0.0781198
X-RAY DIFFRACTIONf_plane_restr0.0045244
X-RAY DIFFRACTIONf_dihedral_angle_d25.1251531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.29171350.29372584X-RAY DIFFRACTION97.81
1.38-1.420.26281400.26242633X-RAY DIFFRACTION98.97
1.42-1.460.27451410.24842643X-RAY DIFFRACTION99.78
1.46-1.510.21561440.22162685X-RAY DIFFRACTION99.89
1.51-1.560.24921420.21272647X-RAY DIFFRACTION100
1.56-1.630.21731420.21482661X-RAY DIFFRACTION100
1.63-1.70.23231420.21592662X-RAY DIFFRACTION100
1.7-1.790.23461440.21132669X-RAY DIFFRACTION99.89
1.79-1.90.25241390.20732678X-RAY DIFFRACTION100
1.9-2.050.21971430.19052692X-RAY DIFFRACTION100
2.05-2.260.20571460.18272692X-RAY DIFFRACTION99.96
2.26-2.580.18811430.17962687X-RAY DIFFRACTION99.86
2.58-3.250.26411440.17812730X-RAY DIFFRACTION99.9
3.25-45.330.2021540.16942817X-RAY DIFFRACTION99.73

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