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

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Basic information

Entry
Database: PDB / ID: 7krh
TitleCrystal structure of the MarR family transcriptional regulator from Variovorax paradoxus with S28A and R46A mutations
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
Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionNov 19, 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)21,1564
Polymers20,8681
Non-polymers2883
Water2,036113
1
A: Transcriptional regulator, MarR family
hetero molecules

A: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3128
Polymers41,7352
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.899, 113.476, 115.125
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-320-

HOH

21A-344-

HOH

31A-393-

HOH

41A-407-

HOH

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Components

#1: Protein Transcriptional regulator, MarR family


Mass: 20867.600 Da / Num. of mol.: 1 / Mutation: S28A, R46A
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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris: HCl, pH 8.5, 2 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 1.41→45.41 Å / Num. obs: 28873 / % possible obs: 99.73 % / Redundancy: 2 % / Biso Wilson estimate: 24.59 Å2 / CC1/2: 1 / Net I/σ(I): 25.59
Reflection shellResolution: 1.5→1.554 Å / Num. unique obs: 2837 / CC1/2: 0.838

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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: 1.5→30.31 Å / SU ML: 0.1618 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7497
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2226 2000 6.93 %
Rwork0.1962 26867 -
obs0.198 28867 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.77 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 0 15 113 1256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761332
X-RAY DIFFRACTIONf_angle_d0.91091823
X-RAY DIFFRACTIONf_chiral_restr0.0503201
X-RAY DIFFRACTIONf_plane_restr0.0048246
X-RAY DIFFRACTIONf_dihedral_angle_d27.62528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.30181380.27371879X-RAY DIFFRACTION99.85
1.54-1.580.27481460.2521910X-RAY DIFFRACTION99.9
1.58-1.630.29491420.2461897X-RAY DIFFRACTION99.76
1.63-1.680.26991400.23891886X-RAY DIFFRACTION99.9
1.68-1.740.27731410.24361899X-RAY DIFFRACTION99.85
1.74-1.810.27571450.2291924X-RAY DIFFRACTION99.81
1.81-1.890.23031380.22491905X-RAY DIFFRACTION99.9
1.89-1.990.23171460.21071913X-RAY DIFFRACTION99.85
1.99-2.110.20261340.2031918X-RAY DIFFRACTION99.66
2.11-2.280.21691490.20111913X-RAY DIFFRACTION99.71
2.28-2.510.22411390.19041933X-RAY DIFFRACTION99.62
2.51-2.870.24651450.20091927X-RAY DIFFRACTION99.95
2.87-3.610.20371470.18721940X-RAY DIFFRACTION99.52
3.61-30.310.20731500.17652023X-RAY DIFFRACTION99.31

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