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

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Basic information

Entry
Database: PDB / ID: 7kjl
TitleCrystal structure of the MarR family transcriptional regulator from Variovorax paradoxus bound to Salicylic 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
2-HYDROXYBENZOIC ACID / Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 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)21,3965
Polymers20,9701
Non-polymers4264
Water1,76598
1
A: Transcriptional regulator, MarR family
hetero molecules

A: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,79210
Polymers41,9392
Non-polymers8538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)54.826, 113.864, 116.416
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-337-

HOH

21A-375-

HOH

31A-387-

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-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium 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: 1.6→40.7 Å / Num. obs: 24031 / % possible obs: 99.13 % / Redundancy: 2 % / Biso Wilson estimate: 27.02 Å2 / CC1/2: 1 / Net I/σ(I): 22.68
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 2237 / CC1/2: 0.554

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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: 1.6→40.7 Å / SU ML: 0.1747 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2162 1998 8.31 %
Rwork0.1868 22033 -
obs0.1892 24031 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.58 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1125 0 25 98 1248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581279
X-RAY DIFFRACTIONf_angle_d0.74561740
X-RAY DIFFRACTIONf_chiral_restr0.0478189
X-RAY DIFFRACTIONf_plane_restr0.004233
X-RAY DIFFRACTIONf_dihedral_angle_d30.616184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.31551360.30961433X-RAY DIFFRACTION91.92
1.64-1.680.32411320.28061543X-RAY DIFFRACTION97.33
1.68-1.730.27291480.26131535X-RAY DIFFRACTION99.41
1.73-1.790.25871380.22371578X-RAY DIFFRACTION99.94
1.79-1.850.23221430.221577X-RAY DIFFRACTION100
1.85-1.930.21521410.20421562X-RAY DIFFRACTION100
1.93-2.020.23961400.19791590X-RAY DIFFRACTION99.88
2.02-2.120.22191470.19691558X-RAY DIFFRACTION100
2.12-2.260.19571410.18411593X-RAY DIFFRACTION100
2.26-2.430.19741420.19011579X-RAY DIFFRACTION100
2.43-2.670.24041450.19171593X-RAY DIFFRACTION99.89
2.67-3.060.21791450.18321608X-RAY DIFFRACTION99.94
3.06-3.850.19581480.16781599X-RAY DIFFRACTION99.83
3.86-40.70.20951520.17341685X-RAY DIFFRACTION99.78

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